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50 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
51 const t_mdatoms *mdatoms, const t_blocka *excl,
52 rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
53 real lambda, real *dvdlambda)
55 /* Calculate the reaction-field energy correction for this node:
56 * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
57 * and force correction for all excluded pairs, including self pairs.
59 int top, i, j, j1, j2, k, ki;
60 double q2sumA, q2sumB, ener;
61 const real *chargeA, *chargeB;
62 real ek, ec, L1, qiA, qiB, qqA, qqB, qqL, v;
67 int end = mdatoms->homenr;
69 gmx_bool bMolPBC = fr->bMolPBC;
73 /* For test particle insertion we only correct for the test molecule */
74 start = mdatoms->nr - fr->n_tpi;
77 ek = fr->epsfac*fr->k_rf;
78 ec = fr->epsfac*fr->c_rf;
79 chargeA = mdatoms->chargeA;
80 chargeB = mdatoms->chargeB;
96 if (mdatoms->nChargePerturbed == 0)
98 for (i = start; i < niat; i++)
105 /* Do the exclusions */
107 j2 = excl->index[i+1];
108 for (j = j1; j < j2; j++)
113 qqA = qiA*chargeA[k];
118 rvec_sub(x[i], x[k], dx);
119 ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
124 ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
128 rvec_sub(x[i], x[k], dx);
130 ener += qqA*(ek*norm2(dx) - ec);
131 svmul(-2*qqA*ek, dx, df);
134 rvec_inc(fshift[ki], df);
135 rvec_dec(fshift[CENTRAL], df);
140 ener += -0.5*ec*q2sumA;
145 for (i = start; i < niat; i++)
154 /* Do the exclusions */
156 j2 = excl->index[i+1];
157 for (j = j1; j < j2; j++)
162 qqA = qiA*chargeA[k];
163 qqB = qiB*chargeB[k];
164 if (qqA != 0 || qqB != 0)
166 qqL = L1*qqA + lambda*qqB;
169 rvec_sub(x[i], x[k], dx);
170 ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
175 ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
179 rvec_sub(x[i], x[k], dx);
181 v = ek*norm2(dx) - ec;
183 svmul(-2*qqL*ek, dx, df);
186 rvec_inc(fshift[ki], df);
187 rvec_dec(fshift[CENTRAL], df);
188 *dvdlambda += (qqB - qqA)*v;
193 ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
194 *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
199 fprintf(debug, "RF exclusion energy: %g\n", ener);
205 void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf, real Rc, real Temp,
206 real zsq, matrix box,
207 real *kappa, real *krf, real *crf)
209 /* Compute constants for Generalized reaction field */
210 real k1, k2, I, vol, rmin;
217 /* Consistency check */
220 gmx_fatal(FARGS, "Temperature is %f while using"
221 " Generalized Reaction Field\n", Temp);
223 /* Ionic strength (only needed for eelGRF */
225 *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
233 /* eps == 0 signals infinite dielectric */
236 *krf = 1/(2*Rc*Rc*Rc);
241 k2 = eps_rf*sqr((real)(*kappa*Rc));
243 *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
245 *crf = 1/Rc + *krf*Rc*Rc;
246 rmin = pow(*krf*2.0, -1.0/3.0);
252 please_cite(fplog, "Tironi95a");
253 fprintf(fplog, "%s:\n"
254 "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
255 "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
256 eel_names[eel], eps_rf, I, vol, *kappa, Rc, *krf, *crf,
261 fprintf(fplog, "%s:\n"
262 "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
263 eel_names[eel], eps_rf, Rc, *krf, *crf, ONE_4PI_EPS0/eps_r);
266 "The electrostatics potential has its minimum at r = %g\n",
272 void init_generalized_rf(FILE *fplog,
273 const gmx_mtop_t *mtop, const t_inputrec *ir,
277 real q, zsq, nrdf, T;
278 const gmx_moltype_t *molt;
281 if (ir->efep != efepNO && fplog)
283 fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
286 for (mb = 0; mb < mtop->nmolblock; mb++)
288 molt = &mtop->moltype[mtop->molblock[mb].type];
290 for (i = 0; (i < cgs->nr); i++)
293 for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
295 q += molt->atoms.atom[j].q;
297 zsq += mtop->molblock[mb].nmol*q*q;
304 for (i = 0; (i < ir->opts.ngtc); i++)
306 nrdf += ir->opts.nrdf[i];
307 T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
311 gmx_fatal(FARGS, "No degrees of freedom!");