src/gromacs/mdlib/rf_util.c

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  37 #include "config.h"
  38
  39 #include "typedefs.h"
  40 #include "force.h"
  41 #include "names.h"
  42 #include "copyrite.h"
  43
  44 #include "gromacs/pbcutil/ishift.h"
  45 #include "gromacs/pbcutil/mshift.h"
  46 #include "gromacs/pbcutil/pbc.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/vec.h"
  49
  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)
  54 {
  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.
  58      */
  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;
  63     rvec        dx, df;
  64     atom_id    *AA;
  65     ivec        dt;
  66     int         start = 0;
  67     int         end   = mdatoms->homenr;
  68     int         niat;
  69     gmx_bool    bMolPBC = fr->bMolPBC;
  70
  71     if (fr->n_tpi)
  72     {
  73         /* For test particle insertion we only correct for the test molecule */
  74         start = mdatoms->nr - fr->n_tpi;
  75     }
  76
  77     ek      = fr->epsfac*fr->k_rf;
  78     ec      = fr->epsfac*fr->c_rf;
  79     chargeA = mdatoms->chargeA;
  80     chargeB = mdatoms->chargeB;
  81     AA      = excl->a;
  82     ki      = CENTRAL;
  83
  84     if (fr->bDomDec)
  85     {
  86         niat = excl->nr;
  87     }
  88     else
  89     {
  90         niat = end;
  91     }
  92
  93     q2sumA = 0;
  94     q2sumB = 0;
  95     ener   = 0;
  96     if (mdatoms->nChargePerturbed == 0)
  97     {
  98         for (i = start; i < niat; i++)
  99         {
 100             qiA = chargeA[i];
 101             if (i < end)
 102             {
 103                 q2sumA += qiA*qiA;
 104             }
 105             /* Do the exclusions */
 106             j1  = excl->index[i];
 107             j2  = excl->index[i+1];
 108             for (j = j1; j < j2; j++)
 109             {
 110                 k = AA[j];
 111                 if (k > i)
 112                 {
 113                     qqA = qiA*chargeA[k];
 114                     if (qqA != 0)
 115                     {
 116                         if (g)
 117                         {
 118                             rvec_sub(x[i], x[k], dx);
 119                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 120                             ki = IVEC2IS(dt);
 121                         }
 122                         else if (bMolPBC)
 123                         {
 124                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 125                         }
 126                         else
 127                         {
 128                             rvec_sub(x[i], x[k], dx);
 129                         }
 130                         ener += qqA*(ek*norm2(dx) - ec);
 131                         svmul(-2*qqA*ek, dx, df);
 132                         rvec_inc(f[i], df);
 133                         rvec_dec(f[k], df);
 134                         rvec_inc(fshift[ki], df);
 135                         rvec_dec(fshift[CENTRAL], df);
 136                     }
 137                 }
 138             }
 139         }
 140         ener += -0.5*ec*q2sumA;
 141     }
 142     else
 143     {
 144         L1 = 1.0 - lambda;
 145         for (i = start; i < niat; i++)
 146         {
 147             qiA = chargeA[i];
 148             qiB = chargeB[i];
 149             if (i < end)
 150             {
 151                 q2sumA += qiA*qiA;
 152                 q2sumB += qiB*qiB;
 153             }
 154             /* Do the exclusions */
 155             j1  = excl->index[i];
 156             j2  = excl->index[i+1];
 157             for (j = j1; j < j2; j++)
 158             {
 159                 k = AA[j];
 160                 if (k > i)
 161                 {
 162                     qqA = qiA*chargeA[k];
 163                     qqB = qiB*chargeB[k];
 164                     if (qqA != 0 || qqB != 0)
 165                     {
 166                         qqL = L1*qqA + lambda*qqB;
 167                         if (g)
 168                         {
 169                             rvec_sub(x[i], x[k], dx);
 170                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 171                             ki = IVEC2IS(dt);
 172                         }
 173                         else if (bMolPBC)
 174                         {
 175                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 176                         }
 177                         else
 178                         {
 179                             rvec_sub(x[i], x[k], dx);
 180                         }
 181                         v     = ek*norm2(dx) - ec;
 182                         ener += qqL*v;
 183                         svmul(-2*qqL*ek, dx, df);
 184                         rvec_inc(f[i], df);
 185                         rvec_dec(f[k], df);
 186                         rvec_inc(fshift[ki], df);
 187                         rvec_dec(fshift[CENTRAL], df);
 188                         *dvdlambda += (qqB - qqA)*v;
 189                     }
 190                 }
 191             }
 192         }
 193         ener       += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
 194         *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
 195     }
 196
 197     if (debug)
 198     {
 199         fprintf(debug, "RF exclusion energy: %g\n", ener);
 200     }
 201
 202     return ener;
 203 }
 204
 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)
 208 {
 209     /* Compute constants for Generalized reaction field */
 210     real   k1, k2, I, vol, rmin;
 211
 212     if (EEL_RF(eel))
 213     {
 214         vol     = det(box);
 215         if (eel == eelGRF)
 216         {
 217             /* Consistency check */
 218             if (Temp <= 0.0)
 219             {
 220                 gmx_fatal(FARGS, "Temperature is %f while using"
 221                           " Generalized Reaction Field\n", Temp);
 222             }
 223             /* Ionic strength (only needed for eelGRF */
 224             I       = 0.5*zsq/vol;
 225             *kappa  = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
 226         }
 227         else
 228         {
 229             I      = 0;
 230             *kappa = 0;
 231         }
 232
 233         /* eps == 0 signals infinite dielectric */
 234         if (eps_rf == 0)
 235         {
 236             *krf = 1/(2*Rc*Rc*Rc);
 237         }
 238         else
 239         {
 240             k1   = 1 + *kappa*Rc;
 241             k2   = eps_rf*sqr((real)(*kappa*Rc));
 242
 243             *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
 244         }
 245         *crf   = 1/Rc + *krf*Rc*Rc;
 246         rmin   = pow(*krf*2.0, -1.0/3.0);
 247
 248         if (fplog)
 249         {
 250             if (eel == eelGRF)
 251             {
 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,
 257                         ONE_4PI_EPS0/eps_r);
 258             }
 259             else
 260             {
 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);
 264             }
 265             fprintf(fplog,
 266                     "The electrostatics potential has its minimum at r = %g\n",
 267                     rmin);
 268         }
 269     }
 270 }
 271
 272 void init_generalized_rf(FILE *fplog,
 273                          const gmx_mtop_t *mtop, const t_inputrec *ir,
 274                          t_forcerec *fr)
 275 {
 276     int                  mb, i, j;
 277     real                 q, zsq, nrdf, T;
 278     const gmx_moltype_t *molt;
 279     const t_block       *cgs;
 280
 281     if (ir->efep != efepNO && fplog)
 282     {
 283         fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
 284     }
 285     zsq = 0.0;
 286     for (mb = 0; mb < mtop->nmolblock; mb++)
 287     {
 288         molt = &mtop->moltype[mtop->molblock[mb].type];
 289         cgs  = &molt->cgs;
 290         for (i = 0; (i < cgs->nr); i++)
 291         {
 292             q = 0;
 293             for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
 294             {
 295                 q += molt->atoms.atom[j].q;
 296             }
 297             zsq += mtop->molblock[mb].nmol*q*q;
 298         }
 299         fr->zsquare = zsq;
 300     }
 301
 302     T    = 0.0;
 303     nrdf = 0.0;
 304     for (i = 0; (i < ir->opts.ngtc); i++)
 305     {
 306         nrdf += ir->opts.nrdf[i];
 307         T    += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
 308     }
 309     if (nrdf == 0)
 310     {
 311         gmx_fatal(FARGS, "No degrees of freedom!");
 312     }
 313     fr->temp   = T/nrdf;
 314 }