src/gromacs/ewald/ewald.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 /*! \internal \file
  38  *
  39  * \brief This file contains function definitions necessary for
  40  * computing energies and forces for the plain-Ewald long-ranged part,
  41  * and the correction for overall system charge for all Ewald-family
  42  * methods.
  43  *
  44  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  45  * \author Mark Abraham <mark.j.abraham@gmail.com>
  46  * \ingroup module_ewald
  47  */
  48 #include "gmxpre.h"
  49
  50 #include "ewald.h"
  51
  52 #include <stdio.h>
  53
  54 #include <cmath>
  55 #include <cstdlib>
  56
  57 #include <algorithm>
  58
  59 #include "gromacs/ewald/ewald-utils.h"
  60 #include "gromacs/math/functions.h"
  61 #include "gromacs/math/gmxcomplex.h"
  62 #include "gromacs/math/units.h"
  63 #include "gromacs/math/utilities.h"
  64 #include "gromacs/math/vec.h"
  65 #include "gromacs/math/vectypes.h"
  66 #include "gromacs/mdtypes/commrec.h"
  67 #include "gromacs/mdtypes/forcerec.h"
  68 #include "gromacs/mdtypes/inputrec.h"
  69 #include "gromacs/mdtypes/md_enums.h"
  70 #include "gromacs/utility/fatalerror.h"
  71 #include "gromacs/utility/smalloc.h"
  72
  73 struct gmx_ewald_tab_t
  74 {
  75     int        nx, ny, nz, kmax;
  76     cvec     **eir;
  77     t_complex *tab_xy, *tab_qxyz;
  78 };
  79
  80 void init_ewald_tab(struct gmx_ewald_tab_t **et, const t_inputrec *ir, FILE *fp)
  81 {
  82     snew(*et, 1);
  83     if (fp)
  84     {
  85         fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
  86     }
  87
  88     (*et)->nx       = ir->nkx+1;
  89     (*et)->ny       = ir->nky+1;
  90     (*et)->nz       = ir->nkz+1;
  91     (*et)->kmax     = std::max((*et)->nx, std::max((*et)->ny, (*et)->nz));
  92     (*et)->eir      = nullptr;
  93     (*et)->tab_xy   = nullptr;
  94     (*et)->tab_qxyz = nullptr;
  95 }
  96
  97 //! Calculates wave vectors.
  98 static void calc_lll(const rvec box, rvec lll)
  99 {
 100     lll[XX] = 2.0*M_PI/box[XX];
 101     lll[YY] = 2.0*M_PI/box[YY];
 102     lll[ZZ] = 2.0*M_PI/box[ZZ];
 103 }
 104
 105 //! Make tables for the structure factor parts
 106 static void tabulateStructureFactors(int natom, rvec x[], int kmax, cvec **eir, rvec lll)
 107 {
 108     int  i, j, m;
 109
 110     if (kmax < 1)
 111     {
 112         printf("Go away! kmax = %d\n", kmax);
 113         exit(1);
 114     }
 115
 116     for (i = 0; (i < natom); i++)
 117     {
 118         for (m = 0; (m < 3); m++)
 119         {
 120             eir[0][i][m].re = 1;
 121             eir[0][i][m].im = 0;
 122         }
 123
 124         for (m = 0; (m < 3); m++)
 125         {
 126             eir[1][i][m].re = cos(x[i][m]*lll[m]);
 127             eir[1][i][m].im = sin(x[i][m]*lll[m]);
 128         }
 129         for (j = 2; (j < kmax); j++)
 130         {
 131             for (m = 0; (m < 3); m++)
 132             {
 133                 eir[j][i][m] = cmul(eir[j-1][i][m], eir[1][i][m]);
 134             }
 135         }
 136     }
 137 }
 138
 139 real do_ewald(t_inputrec *ir,
 140               rvec x[],        rvec f[],
 141               real chargeA[],  real chargeB[],
 142               matrix box,
 143               t_commrec *cr,   int natoms,
 144               matrix lrvir,    real ewaldcoeff,
 145               real lambda,     real *dvdlambda,
 146               struct gmx_ewald_tab_t *et)
 147 {
 148     real     factor     = -1.0/(4*ewaldcoeff*ewaldcoeff);
 149     real    *charge, energy_AB[2], energy;
 150     rvec     lll;
 151     int      lowiy, lowiz, ix, iy, iz, n, q;
 152     real     tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
 153     gmx_bool bFreeEnergy;
 154
 155     if (cr != nullptr)
 156     {
 157         if (PAR(cr))
 158         {
 159             gmx_fatal(FARGS, "No parallel Ewald. Use PME instead.\n");
 160         }
 161     }
 162
 163     /* Scale box with Ewald wall factor */
 164     matrix          scaledBox;
 165     EwaldBoxZScaler boxScaler(*ir);
 166     boxScaler.scaleBox(box, scaledBox);
 167
 168     rvec boxDiag;
 169     for (int i = 0; (i < DIM); i++)
 170     {
 171         boxDiag[i] = scaledBox[i][i];
 172     }
 173
 174     /* 1/(Vol*e0) */
 175     real scaleRecip = 4.0*M_PI/(boxDiag[XX]*boxDiag[YY]*boxDiag[ZZ])*ONE_4PI_EPS0/ir->epsilon_r;
 176
 177     if (!et->eir) /* allocate if we need to */
 178     {
 179         snew(et->eir, et->kmax);
 180         for (n = 0; n < et->kmax; n++)
 181         {
 182             snew(et->eir[n], natoms);
 183         }
 184         snew(et->tab_xy, natoms);
 185         snew(et->tab_qxyz, natoms);
 186     }
 187
 188     bFreeEnergy = (ir->efep != efepNO);
 189
 190     clear_mat(lrvir);
 191
 192     calc_lll(boxDiag, lll);
 193     tabulateStructureFactors(natoms, x, et->kmax, et->eir, lll);
 194
 195     for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
 196     {
 197         if (!bFreeEnergy)
 198         {
 199             charge = chargeA;
 200             scale  = 1.0;
 201         }
 202         else if (q == 0)
 203         {
 204             charge = chargeA;
 205             scale  = 1.0 - lambda;
 206         }
 207         else
 208         {
 209             charge = chargeB;
 210             scale  = lambda;
 211         }
 212         lowiy        = 0;
 213         lowiz        = 1;
 214         energy_AB[q] = 0;
 215         for (ix = 0; ix < et->nx; ix++)
 216         {
 217             mx = ix*lll[XX];
 218             for (iy = lowiy; iy < et->ny; iy++)
 219             {
 220                 my = iy*lll[YY];
 221                 if (iy >= 0)
 222                 {
 223                     for (n = 0; n < natoms; n++)
 224                     {
 225                         et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
 226                     }
 227                 }
 228                 else
 229                 {
 230                     for (n = 0; n < natoms; n++)
 231                     {
 232                         et->tab_xy[n] = cmul(et->eir[ix][n][XX], conjugate(et->eir[-iy][n][YY]));
 233                     }
 234                 }
 235                 for (iz = lowiz; iz < et->nz; iz++)
 236                 {
 237                     mz  = iz*lll[ZZ];
 238                     m2  = mx*mx+my*my+mz*mz;
 239                     ak  = exp(m2*factor)/m2;
 240                     akv = 2.0*ak*(1.0/m2-factor);
 241                     if (iz >= 0)
 242                     {
 243                         for (n = 0; n < natoms; n++)
 244                         {
 245                             et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n],
 246                                                                     et->eir[iz][n][ZZ]));
 247                         }
 248                     }
 249                     else
 250                     {
 251                         for (n = 0; n < natoms; n++)
 252                         {
 253                             et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n],
 254                                                                     conjugate(et->eir[-iz][n][ZZ])));
 255                         }
 256                     }
 257
 258                     cs = ss = 0;
 259                     for (n = 0; n < natoms; n++)
 260                     {
 261                         cs += et->tab_qxyz[n].re;
 262                         ss += et->tab_qxyz[n].im;
 263                     }
 264                     energy_AB[q]  += ak*(cs*cs+ss*ss);
 265                     tmp            = scale*akv*(cs*cs+ss*ss);
 266                     lrvir[XX][XX] -= tmp*mx*mx;
 267                     lrvir[XX][YY] -= tmp*mx*my;
 268                     lrvir[XX][ZZ] -= tmp*mx*mz;
 269                     lrvir[YY][YY] -= tmp*my*my;
 270                     lrvir[YY][ZZ] -= tmp*my*mz;
 271                     lrvir[ZZ][ZZ] -= tmp*mz*mz;
 272                     for (n = 0; n < natoms; n++)
 273                     {
 274                         /*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
 275                         tmp       = scale*ak*(cs*et->tab_qxyz[n].im-ss*et->tab_qxyz[n].re);
 276                         f[n][XX] += tmp*mx*2*scaleRecip;
 277                         f[n][YY] += tmp*my*2*scaleRecip;
 278                         f[n][ZZ] += tmp*mz*2*scaleRecip;
 279 #if 0
 280                         f[n][XX] += tmp*mx;
 281                         f[n][YY] += tmp*my;
 282                         f[n][ZZ] += tmp*mz;
 283 #endif
 284                     }
 285                     lowiz = 1-et->nz;
 286                 }
 287                 lowiy = 1-et->ny;
 288             }
 289         }
 290     }
 291
 292     if (!bFreeEnergy)
 293     {
 294         energy = energy_AB[0];
 295     }
 296     else
 297     {
 298         energy      = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
 299         *dvdlambda += scaleRecip*(energy_AB[1] - energy_AB[0]);
 300     }
 301
 302     lrvir[XX][XX] = -0.5*scaleRecip*(lrvir[XX][XX]+energy);
 303     lrvir[XX][YY] = -0.5*scaleRecip*(lrvir[XX][YY]);
 304     lrvir[XX][ZZ] = -0.5*scaleRecip*(lrvir[XX][ZZ]);
 305     lrvir[YY][YY] = -0.5*scaleRecip*(lrvir[YY][YY]+energy);
 306     lrvir[YY][ZZ] = -0.5*scaleRecip*(lrvir[YY][ZZ]);
 307     lrvir[ZZ][ZZ] = -0.5*scaleRecip*(lrvir[ZZ][ZZ]+energy);
 308
 309     lrvir[YY][XX] = lrvir[XX][YY];
 310     lrvir[ZZ][XX] = lrvir[XX][ZZ];
 311     lrvir[ZZ][YY] = lrvir[YY][ZZ];
 312
 313     energy *= scaleRecip;
 314
 315     return energy;
 316 }
 317
 318 real ewald_charge_correction(t_commrec *cr, t_forcerec *fr, real lambda,
 319                              matrix box,
 320                              real *dvdlambda, tensor vir)
 321
 322 {
 323     real vol, fac, qs2A, qs2B, vc, enercorr;
 324     int  d;
 325
 326     if (MASTER(cr))
 327     {
 328         /* Apply charge correction */
 329         vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
 330
 331         fac = M_PI*ONE_4PI_EPS0/(fr->ic->epsilon_r*2.0*vol*vol*gmx::square(fr->ic->ewaldcoeff_q));
 332
 333         qs2A = fr->qsum[0]*fr->qsum[0];
 334         qs2B = fr->qsum[1]*fr->qsum[1];
 335
 336         vc = (qs2A*(1 - lambda) + qs2B*lambda)*fac;
 337
 338         enercorr = -vol*vc;
 339
 340         *dvdlambda += -vol*(qs2B - qs2A)*fac;
 341
 342         for (d = 0; d < DIM; d++)
 343         {
 344             vir[d][d] += vc;
 345         }
 346
 347         if (debug)
 348         {
 349             fprintf(debug, "Total charge correction: Vcharge=%g\n", enercorr);
 350         }
 351     }
 352     else
 353     {
 354         enercorr = 0;
 355     }
 356
 357     return enercorr;
 358 }