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33 * GROwing Monsters And Cloning Shrimps
48 real RF_excl_correction(FILE *log,
49 const t_forcerec *fr,t_graph *g,
50 const t_mdatoms *mdatoms,const t_blocka *excl,
51 rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
52 real lambda,real *dvdlambda)
54 /* Calculate the reaction-field energy correction for this node:
55 * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
56 * and force correction for all excluded pairs, including self pairs.
58 int top,i,j,j1,j2,k,ki;
59 double q2sumA,q2sumB,ener;
60 const real *chargeA,*chargeB;
61 real ek,ec,L1,qiA,qiB,qqA,qqB,qqL,v;
65 int start = mdatoms->start;
66 int end = mdatoms->homenr+start;
68 gmx_bool bMolPBC = fr->bMolPBC;
71 /* For test particle insertion we only correct for the test molecule */
72 start = mdatoms->nr - fr->n_tpi;
74 ek = fr->epsfac*fr->k_rf;
75 ec = fr->epsfac*fr->c_rf;
76 chargeA = mdatoms->chargeA;
77 chargeB = mdatoms->chargeB;
89 if (mdatoms->nChargePerturbed == 0) {
90 for(i=start; i<niat; i++) {
94 /* Do the exclusions */
96 j2 = excl->index[i+1];
97 for(j=j1; j<j2; j++) {
100 qqA = qiA*chargeA[k];
103 rvec_sub(x[i],x[k],dx);
104 ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
106 } else if (bMolPBC) {
107 ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
109 rvec_sub(x[i],x[k],dx);
110 ener += qqA*(ek*norm2(dx) - ec);
111 svmul(-2*qqA*ek,dx,df);
114 rvec_inc(fshift[ki],df);
115 rvec_dec(fshift[CENTRAL],df);
120 ener += -0.5*ec*q2sumA;
123 for(i=start; i<niat; i++) {
130 /* Do the exclusions */
132 j2 = excl->index[i+1];
133 for(j=j1; j<j2; j++) {
136 qqA = qiA*chargeA[k];
137 qqB = qiB*chargeB[k];
138 if (qqA != 0 || qqB != 0) {
139 qqL = L1*qqA + lambda*qqB;
141 rvec_sub(x[i],x[k],dx);
142 ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
144 } else if (bMolPBC) {
145 ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
147 rvec_sub(x[i],x[k],dx);
148 v = ek*norm2(dx) - ec;
150 svmul(-2*qqL*ek,dx,df);
153 rvec_inc(fshift[ki],df);
154 rvec_dec(fshift[CENTRAL],df);
155 *dvdlambda += (qqB - qqA)*v;
160 ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
161 *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
165 fprintf(debug,"RF exclusion energy: %g\n",ener);
170 void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,real Rc,real Temp,
172 real *kappa,real *krf,real *crf)
174 /* Compute constants for Generalized reaction field */
175 real k1,k2,I,vol,rmin;
180 /* Consistency check */
182 gmx_fatal(FARGS,"Temperature is %f while using"
183 " Generalized Reaction Field\n",Temp);
184 /* Ionic strength (only needed for eelGRF */
186 *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
193 /* eps == 0 signals infinite dielectric */
195 *krf = 1/(2*Rc*Rc*Rc);
198 k2 = eps_rf*sqr((real)(*kappa*Rc));
200 *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
202 *crf = 1/Rc + *krf*Rc*Rc;
203 rmin = pow(*krf*2.0,-1.0/3.0);
207 please_cite(fplog,"Tironi95a");
208 fprintf(fplog,"%s:\n"
209 "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
210 "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
211 eel_names[eel],eps_rf,I,vol,*kappa,Rc,*krf,*crf,
214 fprintf(fplog,"%s:\n"
215 "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
216 eel_names[eel],eps_rf,Rc,*krf,*crf,ONE_4PI_EPS0/eps_r);
219 "The electrostatics potential has its minimum at r = %g\n",
225 void init_generalized_rf(FILE *fplog,
226 const gmx_mtop_t *mtop,const t_inputrec *ir,
231 const gmx_moltype_t *molt;
234 if (ir->efep != efepNO && fplog) {
235 fprintf(fplog,"\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
238 for(mb=0; mb<mtop->nmolblock; mb++) {
239 molt = &mtop->moltype[mtop->molblock[mb].type];
241 for(i=0; (i<cgs->nr); i++) {
243 for(j=cgs->index[i]; (j<cgs->index[i+1]); j++) {
244 q += molt->atoms.atom[j].q;
246 zsq += mtop->molblock[mb].nmol*q*q;
253 for(i=0; (i<ir->opts.ngtc); i++) {
254 nrdf += ir->opts.nrdf[i];
255 T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
258 gmx_fatal(FARGS,"No degrees of freedom!");