src/gromacs/mdlib/rf_util.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40
  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"
  54
  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)
  59 {
  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.
  63      */
  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;
  68     rvec        dx, df;
  69     int        *AA;
  70     ivec        dt;
  71     int         start = 0;
  72     int         end   = mdatoms->homenr;
  73     int         niat;
  74     gmx_bool    bMolPBC = fr->bMolPBC;
  75
  76     if (fr->n_tpi)
  77     {
  78         /* For test particle insertion we only correct for the test molecule */
  79         start = mdatoms->nr - fr->n_tpi;
  80     }
  81
  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;
  86     AA      = excl->a;
  87     ki      = CENTRAL;
  88
  89     if (fr->bDomDec)
  90     {
  91         niat = excl->nr;
  92     }
  93     else
  94     {
  95         niat = end;
  96     }
  97
  98     q2sumA = 0;
  99     q2sumB = 0;
 100     ener   = 0;
 101     if (mdatoms->nChargePerturbed == 0)
 102     {
 103         for (i = start; i < niat; i++)
 104         {
 105             qiA = chargeA[i];
 106             if (i < end)
 107             {
 108                 q2sumA += qiA*qiA;
 109             }
 110             /* Do the exclusions */
 111             j1  = excl->index[i];
 112             j2  = excl->index[i+1];
 113             for (j = j1; j < j2; j++)
 114             {
 115                 k = AA[j];
 116                 if (k > i)
 117                 {
 118                     qqA = qiA*chargeA[k];
 119                     if (qqA != 0)
 120                     {
 121                         if (g)
 122                         {
 123                             rvec_sub(x[i], x[k], dx);
 124                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 125                             ki = IVEC2IS(dt);
 126                         }
 127                         else if (bMolPBC)
 128                         {
 129                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 130                         }
 131                         else
 132                         {
 133                             rvec_sub(x[i], x[k], dx);
 134                         }
 135                         ener += qqA*(ek*norm2(dx) - ec);
 136                         svmul(-2*qqA*ek, dx, df);
 137                         rvec_inc(f[i], df);
 138                         rvec_dec(f[k], df);
 139                         rvec_inc(fshift[ki], df);
 140                         rvec_dec(fshift[CENTRAL], df);
 141                     }
 142                 }
 143             }
 144         }
 145         ener += -0.5*ec*q2sumA;
 146     }
 147     else
 148     {
 149         L1 = 1.0 - lambda;
 150         for (i = start; i < niat; i++)
 151         {
 152             qiA = chargeA[i];
 153             qiB = chargeB[i];
 154             if (i < end)
 155             {
 156                 q2sumA += qiA*qiA;
 157                 q2sumB += qiB*qiB;
 158             }
 159             /* Do the exclusions */
 160             j1  = excl->index[i];
 161             j2  = excl->index[i+1];
 162             for (j = j1; j < j2; j++)
 163             {
 164                 k = AA[j];
 165                 if (k > i)
 166                 {
 167                     qqA = qiA*chargeA[k];
 168                     qqB = qiB*chargeB[k];
 169                     if (qqA != 0 || qqB != 0)
 170                     {
 171                         qqL = L1*qqA + lambda*qqB;
 172                         if (g)
 173                         {
 174                             rvec_sub(x[i], x[k], dx);
 175                             ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
 176                             ki = IVEC2IS(dt);
 177                         }
 178                         else if (bMolPBC)
 179                         {
 180                             ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
 181                         }
 182                         else
 183                         {
 184                             rvec_sub(x[i], x[k], dx);
 185                         }
 186                         v     = ek*norm2(dx) - ec;
 187                         ener += qqL*v;
 188                         svmul(-2*qqL*ek, dx, df);
 189                         rvec_inc(f[i], df);
 190                         rvec_dec(f[k], df);
 191                         rvec_inc(fshift[ki], df);
 192                         rvec_dec(fshift[CENTRAL], df);
 193                         *dvdlambda += (qqB - qqA)*v;
 194                     }
 195                 }
 196             }
 197         }
 198         ener       += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
 199         *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
 200     }
 201
 202     if (debug)
 203     {
 204         fprintf(debug, "RF exclusion energy: %g\n", ener);
 205     }
 206
 207     return ener;
 208 }
 209
 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)
 213 {
 214     /* Compute constants for Generalized reaction field */
 215     real   kappa, k1, k2, I, rmin;
 216     real   vol = 0;
 217
 218     if (EEL_RF(eel))
 219     {
 220         if (eel == eelGRF)
 221         {
 222             /* Consistency check */
 223             if (Temp <= 0.0)
 224             {
 225                 gmx_fatal(FARGS, "Temperature is %f while using"
 226                           " Generalized Reaction Field\n", Temp);
 227             }
 228             /* Ionic strength (only needed for eelGRF */
 229             vol     = det(box);
 230             I       = 0.5*zsq/vol;
 231             kappa   = std::sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
 232         }
 233         else
 234         {
 235             I      = 0;
 236             kappa  = 0;
 237         }
 238
 239         /* eps == 0 signals infinite dielectric */
 240         if (eps_rf == 0)
 241         {
 242             *krf = 1/(2*Rc*Rc*Rc);
 243         }
 244         else
 245         {
 246             k1   = 1 + kappa*Rc;
 247             k2   = eps_rf*gmx::square((real)(kappa*Rc));
 248
 249             *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
 250         }
 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));
 254
 255         if (fplog)
 256         {
 257             if (eel == eelGRF)
 258             {
 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,
 264                         ONE_4PI_EPS0/eps_r);
 265             }
 266             else
 267             {
 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);
 271             }
 272             fprintf(fplog,
 273                     "The electrostatics potential has its minimum at r = %g\n",
 274                     rmin);
 275         }
 276     }
 277 }
 278
 279 void init_generalized_rf(FILE *fplog,
 280                          const gmx_mtop_t *mtop, const t_inputrec *ir,
 281                          t_forcerec *fr)
 282 {
 283     int                  i, j;
 284     real                 q, zsq, nrdf, T;
 285     const gmx_moltype_t *molt;
 286     const t_block       *cgs;
 287
 288     if (ir->efep != efepNO && fplog)
 289     {
 290         fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
 291     }
 292     zsq = 0.0;
 293     for (const gmx_molblock_t &molb : mtop->molblock)
 294     {
 295         molt = &mtop->moltype[molb.type];
 296         cgs  = &molt->cgs;
 297         for (i = 0; (i < cgs->nr); i++)
 298         {
 299             q = 0;
 300             for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
 301             {
 302                 q += molt->atoms.atom[j].q;
 303             }
 304             zsq += molb.nmol*q*q;
 305         }
 306         fr->zsquare = zsq;
 307     }
 308
 309     T    = 0.0;
 310     nrdf = 0.0;
 311     for (i = 0; (i < ir->opts.ngtc); i++)
 312     {
 313         nrdf += ir->opts.nrdf[i];
 314         T    += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
 315     }
 316     if (nrdf == 0)
 317     {
 318         gmx_fatal(FARGS, "No degrees of freedom!");
 319     }
 320     fr->temp   = T/nrdf;
 321 }