src/gromacs/mdlib/rf_util.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40
  41 #include "gromacs/fileio/copyrite.h"
  42 #include "gromacs/legacyheaders/names.h"
  43 #include "gromacs/legacyheaders/types/mdatom.h"
  44 #include "gromacs/math/units.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/mdlib/force.h"
  47 #include "gromacs/pbcutil/ishift.h"
  48 #include "gromacs/pbcutil/mshift.h"
  49 #include "gromacs/pbcutil/pbc.h"
  50 #include "gromacs/utility/fatalerror.h"
  51
  52 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
  53                         const t_mdatoms *mdatoms, const t_blocka *excl,
  54                         rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
  55                         real lambda, real *dvdlambda)
  56 {
  57     /* Calculate the reaction-field energy correction for this node:
  58      * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
  59      * and force correction for all excluded pairs, including self pairs.
  60      */
  61     int         i, j, j1, j2, k, ki;
  62     double      q2sumA, q2sumB, ener;
  63     const real *chargeA, *chargeB;
  64     real        ek, ec, L1, qiA, qiB, qqA, qqB, qqL, v;
  65     rvec        dx, df;
  66     atom_id    *AA;
  67     ivec        dt;
  68     int         start = 0;
  69     int         end   = mdatoms->homenr;
  70     int         niat;
  71     gmx_bool    bMolPBC = fr->bMolPBC;
  72
  73     if (fr->n_tpi)
  74     {
  75         /* For test particle insertion we only correct for the test molecule */
  76         start = mdatoms->nr - fr->n_tpi;
  77     }
  78
  79     ek      = fr->epsfac*fr->k_rf;
  80     ec      = fr->epsfac*fr->c_rf;
  81     chargeA = mdatoms->chargeA;
  82     chargeB = mdatoms->chargeB;
  83     AA      = excl->a;
  84     ki      = CENTRAL;
  85
  86     if (fr->bDomDec)
  87     {
  88         niat = excl->nr;
  89     }
  90     else
  91     {
  92         niat = end;
  93     }
  94
  95     q2sumA = 0;
  96     q2sumB = 0;
  97     ener   = 0;
  98     if (mdatoms->nChargePerturbed == 0)
  99     {
 100         for (i = start; i < niat; i++)
 101         {
 102             qiA = chargeA[i];
 103             if (i < end)
 104             {
 105                 q2sumA += qiA*qiA;
 106             }
 107             /* Do the exclusions */
 108             j1  = excl->index[i];
 109             j2  = excl->index[i+1];
 110             for (j = j1; j < j2; j++)
 111             {
 112                 k = AA[j];
 113                 if (k > i)
 114                 {
 115                     qqA = qiA*chargeA[k];
 116                     if (qqA != 0)
 117                     {
 118                         if (g)
 119                         {
 120                             rvec_sub(x[i], x[k], dx);
 121                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 122                             ki = IVEC2IS(dt);
 123                         }
 124                         else if (bMolPBC)
 125                         {
 126                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 127                         }
 128                         else
 129                         {
 130                             rvec_sub(x[i], x[k], dx);
 131                         }
 132                         ener += qqA*(ek*norm2(dx) - ec);
 133                         svmul(-2*qqA*ek, dx, df);
 134                         rvec_inc(f[i], df);
 135                         rvec_dec(f[k], df);
 136                         rvec_inc(fshift[ki], df);
 137                         rvec_dec(fshift[CENTRAL], df);
 138                     }
 139                 }
 140             }
 141         }
 142         ener += -0.5*ec*q2sumA;
 143     }
 144     else
 145     {
 146         L1 = 1.0 - lambda;
 147         for (i = start; i < niat; i++)
 148         {
 149             qiA = chargeA[i];
 150             qiB = chargeB[i];
 151             if (i < end)
 152             {
 153                 q2sumA += qiA*qiA;
 154                 q2sumB += qiB*qiB;
 155             }
 156             /* Do the exclusions */
 157             j1  = excl->index[i];
 158             j2  = excl->index[i+1];
 159             for (j = j1; j < j2; j++)
 160             {
 161                 k = AA[j];
 162                 if (k > i)
 163                 {
 164                     qqA = qiA*chargeA[k];
 165                     qqB = qiB*chargeB[k];
 166                     if (qqA != 0 || qqB != 0)
 167                     {
 168                         qqL = L1*qqA + lambda*qqB;
 169                         if (g)
 170                         {
 171                             rvec_sub(x[i], x[k], dx);
 172                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 173                             ki = IVEC2IS(dt);
 174                         }
 175                         else if (bMolPBC)
 176                         {
 177                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 178                         }
 179                         else
 180                         {
 181                             rvec_sub(x[i], x[k], dx);
 182                         }
 183                         v     = ek*norm2(dx) - ec;
 184                         ener += qqL*v;
 185                         svmul(-2*qqL*ek, dx, df);
 186                         rvec_inc(f[i], df);
 187                         rvec_dec(f[k], df);
 188                         rvec_inc(fshift[ki], df);
 189                         rvec_dec(fshift[CENTRAL], df);
 190                         *dvdlambda += (qqB - qqA)*v;
 191                     }
 192                 }
 193             }
 194         }
 195         ener       += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
 196         *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
 197     }
 198
 199     if (debug)
 200     {
 201         fprintf(debug, "RF exclusion energy: %g\n", ener);
 202     }
 203
 204     return ener;
 205 }
 206
 207 void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf, real Rc, real Temp,
 208                 real zsq, matrix box,
 209                 real *kappa, real *krf, real *crf)
 210 {
 211     /* Compute constants for Generalized reaction field */
 212     real   k1, k2, I, vol, rmin;
 213
 214     if (EEL_RF(eel))
 215     {
 216         vol     = det(box);
 217         if (eel == eelGRF)
 218         {
 219             /* Consistency check */
 220             if (Temp <= 0.0)
 221             {
 222                 gmx_fatal(FARGS, "Temperature is %f while using"
 223                           " Generalized Reaction Field\n", Temp);
 224             }
 225             /* Ionic strength (only needed for eelGRF */
 226             I       = 0.5*zsq/vol;
 227             *kappa  = std::sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
 228         }
 229         else
 230         {
 231             I      = 0;
 232             *kappa = 0;
 233         }
 234
 235         /* eps == 0 signals infinite dielectric */
 236         if (eps_rf == 0)
 237         {
 238             *krf = 1/(2*Rc*Rc*Rc);
 239         }
 240         else
 241         {
 242             k1   = 1 + *kappa*Rc;
 243             k2   = eps_rf*sqr((real)(*kappa*Rc));
 244
 245             *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
 246         }
 247         *crf   = 1/Rc + *krf*Rc*Rc;
 248         // Make sure we don't lose resolution in pow() by casting real arg to double
 249         rmin   = std::pow(static_cast<double>(*krf*2.0), -1.0/3.0);
 250
 251         if (fplog)
 252         {
 253             if (eel == eelGRF)
 254             {
 255                 please_cite(fplog, "Tironi95a");
 256                 fprintf(fplog, "%s:\n"
 257                         "epsRF = %10g, I   = %10g, volume = %10g, kappa  = %10g\n"
 258                         "rc    = %10g, krf = %10g, crf    = %10g, epsfac = %10g\n",
 259                         eel_names[eel], eps_rf, I, vol, *kappa, Rc, *krf, *crf,
 260                         ONE_4PI_EPS0/eps_r);
 261             }
 262             else
 263             {
 264                 fprintf(fplog, "%s:\n"
 265                         "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
 266                         eel_names[eel], eps_rf, Rc, *krf, *crf, ONE_4PI_EPS0/eps_r);
 267             }
 268             fprintf(fplog,
 269                     "The electrostatics potential has its minimum at r = %g\n",
 270                     rmin);
 271         }
 272     }
 273 }
 274
 275 void init_generalized_rf(FILE *fplog,
 276                          const gmx_mtop_t *mtop, const t_inputrec *ir,
 277                          t_forcerec *fr)
 278 {
 279     int                  mb, i, j;
 280     real                 q, zsq, nrdf, T;
 281     const gmx_moltype_t *molt;
 282     const t_block       *cgs;
 283
 284     if (ir->efep != efepNO && fplog)
 285     {
 286         fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
 287     }
 288     zsq = 0.0;
 289     for (mb = 0; mb < mtop->nmolblock; mb++)
 290     {
 291         molt = &mtop->moltype[mtop->molblock[mb].type];
 292         cgs  = &molt->cgs;
 293         for (i = 0; (i < cgs->nr); i++)
 294         {
 295             q = 0;
 296             for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
 297             {
 298                 q += molt->atoms.atom[j].q;
 299             }
 300             zsq += mtop->molblock[mb].nmol*q*q;
 301         }
 302         fr->zsquare = zsq;
 303     }
 304
 305     T    = 0.0;
 306     nrdf = 0.0;
 307     for (i = 0; (i < ir->opts.ngtc); i++)
 308     {
 309         nrdf += ir->opts.nrdf[i];
 310         T    += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
 311     }
 312     if (nrdf == 0)
 313     {
 314         gmx_fatal(FARGS, "No degrees of freedom!");
 315     }
 316     fr->temp   = T/nrdf;
 317 }