src/mdlib/rf_util.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "force.h"
  42 #include "names.h"
  43 #include "vec.h"
  44 #include "physics.h"
  45 #include "copyrite.h"
  46 #include "pbc.h"
  47
  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)
  53 {
  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.
  57    */
  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;
  62   rvec   dx,df;
  63   atom_id *AA;
  64   ivec   dt;
  65   int    start = mdatoms->start;
  66   int    end   = mdatoms->homenr+start;
  67   int    niat;
  68   gmx_bool   bMolPBC = fr->bMolPBC;
  69
  70   if (fr->n_tpi)
  71     /* For test particle insertion we only correct for the test molecule */
  72     start = mdatoms->nr - fr->n_tpi;
  73
  74   ek = fr->epsfac*fr->k_rf;
  75   ec = fr->epsfac*fr->c_rf;
  76   chargeA = mdatoms->chargeA;
  77   chargeB = mdatoms->chargeB;
  78   AA = excl->a;
  79   ki = CENTRAL;
  80
  81   if (fr->bDomDec)
  82     niat = excl->nr;
  83   else
  84     niat = end;
  85
  86   q2sumA = 0;
  87   q2sumB = 0;
  88   ener = 0;
  89   if (mdatoms->nChargePerturbed == 0) {
  90     for(i=start; i<niat; i++) {
  91       qiA = chargeA[i];
  92       if (i < end)
  93         q2sumA += qiA*qiA;
  94       /* Do the exclusions */
  95       j1  = excl->index[i];
  96       j2  = excl->index[i+1];
  97       for(j=j1; j<j2; j++) {
  98         k = AA[j];
  99         if (k > i) {
 100           qqA = qiA*chargeA[k];
 101           if (qqA != 0) {
 102             if (g) {
 103               rvec_sub(x[i],x[k],dx);
 104               ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
 105               ki=IVEC2IS(dt);
 106             } else if (bMolPBC) {
 107               ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
 108             } else
 109               rvec_sub(x[i],x[k],dx);
 110             ener += qqA*(ek*norm2(dx) - ec);
 111             svmul(-2*qqA*ek,dx,df);
 112             rvec_inc(f[i],df);
 113             rvec_dec(f[k],df);
 114             rvec_inc(fshift[ki],df);
 115             rvec_dec(fshift[CENTRAL],df);
 116           }
 117         }
 118       }
 119     }
 120     ener += -0.5*ec*q2sumA;
 121   } else {
 122     L1 = 1.0 - lambda;
 123     for(i=start; i<niat; i++) {
 124       qiA = chargeA[i];
 125       qiB = chargeB[i];
 126       if (i < end) {
 127         q2sumA += qiA*qiA;
 128         q2sumB += qiB*qiB;
 129       }
 130       /* Do the exclusions */
 131       j1  = excl->index[i];
 132       j2  = excl->index[i+1];
 133       for(j=j1; j<j2; j++) {
 134         k = AA[j];
 135         if (k > i) {
 136           qqA = qiA*chargeA[k];
 137           qqB = qiB*chargeB[k];
 138           if (qqA != 0 || qqB != 0) {
 139             qqL = L1*qqA + lambda*qqB;
 140             if (g) {
 141               rvec_sub(x[i],x[k],dx);
 142               ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
 143               ki=IVEC2IS(dt);
 144             } else if (bMolPBC) {
 145               ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
 146             } else
 147               rvec_sub(x[i],x[k],dx);
 148             v = ek*norm2(dx) - ec;
 149             ener += qqL*v;
 150             svmul(-2*qqL*ek,dx,df);
 151             rvec_inc(f[i],df);
 152             rvec_dec(f[k],df);
 153             rvec_inc(fshift[ki],df);
 154             rvec_dec(fshift[CENTRAL],df);
 155             *dvdlambda += (qqB - qqA)*v;
 156           }
 157         }
 158       }
 159     }
 160     ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
 161     *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
 162   }
 163
 164   if (debug)
 165     fprintf(debug,"RF exclusion energy: %g\n",ener);
 166
 167   return ener;
 168 }
 169
 170 void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,real Rc,real Temp,
 171                 real zsq,matrix box,
 172                 real *kappa,real *krf,real *crf)
 173 {
 174   /* Compute constants for Generalized reaction field */
 175   real   k1,k2,I,vol,rmin;
 176
 177   if (EEL_RF(eel)) {
 178     vol     = det(box);
 179     if (eel == eelGRF) {
 180       /* Consistency check */
 181       if (Temp <= 0.0)
 182         gmx_fatal(FARGS,"Temperature is %f while using"
 183                     " Generalized Reaction Field\n",Temp);
 184       /* Ionic strength (only needed for eelGRF */
 185       I       = 0.5*zsq/vol;
 186       *kappa  = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
 187     }
 188     else {
 189       I      = 0;
 190       *kappa = 0;
 191     }
 192
 193     /* eps == 0 signals infinite dielectric */
 194     if (eps_rf == 0) {
 195       *krf = 1/(2*Rc*Rc*Rc);
 196     } else {
 197       k1   = 1 + *kappa*Rc;
 198       k2   = eps_rf*sqr((real)(*kappa*Rc));
 199
 200       *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
 201     }
 202     *crf   = 1/Rc + *krf*Rc*Rc;
 203     rmin   = pow(*krf*2.0,-1.0/3.0);
 204
 205     if (fplog) {
 206       if (eel == eelGRF) {
 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,
 212                 ONE_4PI_EPS0/eps_r);
 213       } else {
 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);
 217       }
 218       fprintf(fplog,
 219               "The electrostatics potential has its minimum at r = %g\n",
 220               rmin);
 221     }
 222   }
 223 }
 224
 225 void init_generalized_rf(FILE *fplog,
 226                          const gmx_mtop_t *mtop,const t_inputrec *ir,
 227                          t_forcerec *fr)
 228 {
 229   int  mb,i,j;
 230   real q,zsq,nrdf,T;
 231   const gmx_moltype_t *molt;
 232   const t_block *cgs;
 233
 234   if (ir->efep != efepNO && fplog) {
 235     fprintf(fplog,"\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
 236   }
 237   zsq = 0.0;
 238   for(mb=0; mb<mtop->nmolblock; mb++) {
 239     molt = &mtop->moltype[mtop->molblock[mb].type];
 240     cgs  = &molt->cgs;
 241     for(i=0; (i<cgs->nr); i++) {
 242       q = 0;
 243       for(j=cgs->index[i]; (j<cgs->index[i+1]); j++) {
 244         q += molt->atoms.atom[j].q;
 245       }
 246       zsq += mtop->molblock[mb].nmol*q*q;
 247     }
 248     fr->zsquare = zsq;
 249   }
 250
 251   T    = 0.0;
 252   nrdf = 0.0;
 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]);
 256   }
 257   if (nrdf == 0) {
 258     gmx_fatal(FARGS,"No degrees of freedom!");
 259   }
 260   fr->temp   = T/nrdf;
 261 }