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41 #include "gromacs/math/functions.h"
42 #include "gromacs/math/units.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/mdlib/force.h"
45 #include "gromacs/mdtypes/inputrec.h"
46 #include "gromacs/mdtypes/md_enums.h"
47 #include "gromacs/mdtypes/mdatom.h"
48 #include "gromacs/pbcutil/ishift.h"
49 #include "gromacs/pbcutil/mshift.h"
50 #include "gromacs/pbcutil/pbc.h"
51 #include "gromacs/topology/topology.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/pleasecite.h"
55 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
56 const t_mdatoms *mdatoms, const t_blocka *excl,
57 rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
58 real lambda, real *dvdlambda)
60 /* Calculate the reaction-field energy correction for this node:
61 * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
62 * and force correction for all excluded pairs, including self pairs.
64 int i, j, j1, j2, k, ki;
65 double q2sumA, q2sumB, ener;
66 const real *chargeA, *chargeB;
67 real ek, ec, L1, qiA, qiB, qqA, qqB, qqL, v;
72 int end = mdatoms->homenr;
74 gmx_bool bMolPBC = fr->bMolPBC;
78 /* For test particle insertion we only correct for the test molecule */
79 start = mdatoms->nr - fr->n_tpi;
82 ek = fr->ic->epsfac*fr->ic->k_rf;
83 ec = fr->ic->epsfac*fr->ic->c_rf;
84 chargeA = mdatoms->chargeA;
85 chargeB = mdatoms->chargeB;
101 if (mdatoms->nChargePerturbed == 0)
103 for (i = start; i < niat; i++)
110 /* Do the exclusions */
112 j2 = excl->index[i+1];
113 for (j = j1; j < j2; j++)
118 qqA = qiA*chargeA[k];
123 rvec_sub(x[i], x[k], dx);
124 ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
129 ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
133 rvec_sub(x[i], x[k], dx);
135 ener += qqA*(ek*norm2(dx) - ec);
136 svmul(-2*qqA*ek, dx, df);
139 rvec_inc(fshift[ki], df);
140 rvec_dec(fshift[CENTRAL], df);
145 ener += -0.5*ec*q2sumA;
150 for (i = start; i < niat; i++)
159 /* Do the exclusions */
161 j2 = excl->index[i+1];
162 for (j = j1; j < j2; j++)
167 qqA = qiA*chargeA[k];
168 qqB = qiB*chargeB[k];
169 if (qqA != 0 || qqB != 0)
171 qqL = L1*qqA + lambda*qqB;
174 rvec_sub(x[i], x[k], dx);
175 ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
180 ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
184 rvec_sub(x[i], x[k], dx);
186 v = ek*norm2(dx) - ec;
188 svmul(-2*qqL*ek, dx, df);
191 rvec_inc(fshift[ki], df);
192 rvec_dec(fshift[CENTRAL], df);
193 *dvdlambda += (qqB - qqA)*v;
198 ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
199 *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
204 fprintf(debug, "RF exclusion energy: %g\n", ener);
210 void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf, real Rc, real Temp,
211 real zsq, matrix box,
212 real *krf, real *crf)
214 /* Compute constants for Generalized reaction field */
215 real kappa, k1, k2, I, rmin;
222 /* Consistency check */
225 gmx_fatal(FARGS, "Temperature is %f while using"
226 " Generalized Reaction Field\n", Temp);
228 /* Ionic strength (only needed for eelGRF */
231 kappa = std::sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
239 /* eps == 0 signals infinite dielectric */
242 *krf = 1/(2*Rc*Rc*Rc);
247 k2 = eps_rf*gmx::square((real)(kappa*Rc));
249 *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
251 *crf = 1/Rc + *krf*Rc*Rc;
252 // Make sure we don't lose resolution in pow() by casting real arg to double
253 rmin = gmx::invcbrt(static_cast<double>(*krf*2.0));
259 please_cite(fplog, "Tironi95a");
260 fprintf(fplog, "%s:\n"
261 "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
262 "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
263 eel_names[eel], eps_rf, I, vol, kappa, Rc, *krf, *crf,
268 fprintf(fplog, "%s:\n"
269 "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
270 eel_names[eel], eps_rf, Rc, *krf, *crf, ONE_4PI_EPS0/eps_r);
273 "The electrostatics potential has its minimum at r = %g\n",
279 void init_generalized_rf(FILE *fplog,
280 const gmx_mtop_t *mtop, const t_inputrec *ir,
284 real q, zsq, nrdf, T;
285 const gmx_moltype_t *molt;
288 if (ir->efep != efepNO && fplog)
290 fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
293 for (const gmx_molblock_t &molb : mtop->molblock)
295 molt = &mtop->moltype[molb.type];
297 for (i = 0; (i < cgs->nr); i++)
300 for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
302 q += molt->atoms.atom[j].q;
304 zsq += molb.nmol*q*q;
311 for (i = 0; (i < ir->opts.ngtc); i++)
313 nrdf += ir->opts.nrdf[i];
314 T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
318 gmx_fatal(FARGS, "No degrees of freedom!");