src/gromacs/ewald/long-range-correction.c

   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, 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 #include "gmxpre.h"
  38
  39 #include "long-range-correction.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/legacyheaders/macros.h"
  44 #include "gromacs/legacyheaders/names.h"
  45 #include "gromacs/legacyheaders/types/commrec.h"
  46 #include "gromacs/legacyheaders/types/forcerec.h"
  47 #include "gromacs/math/units.h"
  48 #include "gromacs/math/utilities.h"
  49 #include "gromacs/math/vec.h"
  50
  51 /* There's nothing special to do here if just masses are perturbed,
  52  * but if either charge or type is perturbed then the implementation
  53  * requires that B states are defined for both charge and type, and
  54  * does not optimize for the cases where only one changes.
  55  *
  56  * The parameter vectors for B states are left undefined in atoms2md()
  57  * when either FEP is inactive, or when there are no mass/charge/type
  58  * perturbations. The parameter vectors for LJ-PME are likewise
  59  * undefined when LJ-PME is not active. This works because
  60  * bHaveChargeOrTypePerturbed handles the control flow. */
  61 void ewald_LRcorrection(int start, int end,
  62                         t_commrec *cr, int thread, t_forcerec *fr,
  63                         real *chargeA, real *chargeB,
  64                         real *C6A, real *C6B,
  65                         real *sigmaA, real *sigmaB,
  66                         real *sigma3A, real *sigma3B,
  67                         gmx_bool bHaveChargeOrTypePerturbed,
  68                         gmx_bool calc_excl_corr,
  69                         t_blocka *excl, rvec x[],
  70                         matrix box, rvec mu_tot[],
  71                         int ewald_geometry, real epsilon_surface,
  72                         rvec *f, tensor vir_q, tensor vir_lj,
  73                         real *Vcorr_q, real *Vcorr_lj,
  74                         real lambda_q, real lambda_lj,
  75                         real *dvdlambda_q, real *dvdlambda_lj)
  76 {
  77     int         i, i1, i2, j, k, m, iv, jv, q;
  78     atom_id    *AA;
  79     double      Vexcl_q, dvdl_excl_q, dvdl_excl_lj; /* Necessary for precision */
  80     double      Vexcl_lj;
  81     real        one_4pi_eps;
  82     real        v, vc, qiA, qiB, dr2, rinv, enercorr;
  83     real        Vself_q[2], Vself_lj[2], Vdipole[2], rinv2, ewc_q = fr->ewaldcoeff_q, ewcdr;
  84     real        ewc_lj = fr->ewaldcoeff_lj, ewc_lj2 = ewc_lj * ewc_lj;
  85     real        c6Ai   = 0, c6Bi = 0, c6A = 0, c6B = 0, ewcdr2, ewcdr4, c6L = 0, rinv6;
  86     rvec        df, dx, mutot[2], dipcorrA, dipcorrB;
  87     tensor      dxdf_q, dxdf_lj;
  88     real        vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
  89     real        L1_q, L1_lj, dipole_coeff, qqA, qqB, qqL, vr0_q, vr0_lj = 0;
  90     gmx_bool    bMolPBC      = fr->bMolPBC;
  91     gmx_bool    bDoingLBRule = (fr->ljpme_combination_rule == eljpmeLB);
  92
  93     /* This routine can be made faster by using tables instead of analytical interactions
  94      * However, that requires a thorough verification that they are correct in all cases.
  95      */
  96
  97     one_4pi_eps   = ONE_4PI_EPS0/fr->epsilon_r;
  98     vr0_q         = ewc_q*M_2_SQRTPI;
  99     if (EVDW_PME(fr->vdwtype))
 100     {
 101         vr0_lj    = -pow(ewc_lj, 6)/6.0;
 102     }
 103
 104     AA           = excl->a;
 105     Vexcl_q      = 0;
 106     Vexcl_lj     = 0;
 107     dvdl_excl_q  = 0;
 108     dvdl_excl_lj = 0;
 109     Vdipole[0]   = 0;
 110     Vdipole[1]   = 0;
 111     L1_q         = 1.0-lambda_q;
 112     L1_lj        = 1.0-lambda_lj;
 113     /* Note that we have to transform back to gromacs units, since
 114      * mu_tot contains the dipole in debye units (for output).
 115      */
 116     for (i = 0; (i < DIM); i++)
 117     {
 118         mutot[0][i] = mu_tot[0][i]*DEBYE2ENM;
 119         mutot[1][i] = mu_tot[1][i]*DEBYE2ENM;
 120         dipcorrA[i] = 0;
 121         dipcorrB[i] = 0;
 122     }
 123     dipole_coeff = 0;
 124     switch (ewald_geometry)
 125     {
 126         case eewg3D:
 127             if (epsilon_surface != 0)
 128             {
 129                 dipole_coeff =
 130                     2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + fr->epsilon_r)*vol);
 131                 for (i = 0; (i < DIM); i++)
 132                 {
 133                     dipcorrA[i] = 2*dipole_coeff*mutot[0][i];
 134                     dipcorrB[i] = 2*dipole_coeff*mutot[1][i];
 135                 }
 136             }
 137             break;
 138         case eewg3DC:
 139             dipole_coeff = 2*M_PI*one_4pi_eps/vol;
 140             dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
 141             dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
 142             break;
 143         default:
 144             gmx_incons("Unsupported Ewald geometry");
 145             break;
 146     }
 147     if (debug)
 148     {
 149         fprintf(debug, "dipcorr = %8.3f  %8.3f  %8.3f\n",
 150                 dipcorrA[XX], dipcorrA[YY], dipcorrA[ZZ]);
 151         fprintf(debug, "mutot   = %8.3f  %8.3f  %8.3f\n",
 152                 mutot[0][XX], mutot[0][YY], mutot[0][ZZ]);
 153     }
 154     clear_mat(dxdf_q);
 155     if (EVDW_PME(fr->vdwtype))
 156     {
 157         clear_mat(dxdf_lj);
 158     }
 159     if ((calc_excl_corr || dipole_coeff != 0) && !bHaveChargeOrTypePerturbed)
 160     {
 161         for (i = start; (i < end); i++)
 162         {
 163             /* Initiate local variables (for this i-particle) to 0 */
 164             qiA = chargeA[i]*one_4pi_eps;
 165             if (EVDW_PME(fr->vdwtype))
 166             {
 167                 c6Ai = C6A[i];
 168                 if (bDoingLBRule)
 169                 {
 170                     c6Ai *= sigma3A[i];
 171                 }
 172             }
 173             if (calc_excl_corr)
 174             {
 175                 i1  = excl->index[i];
 176                 i2  = excl->index[i+1];
 177
 178                 /* Loop over excluded neighbours */
 179                 for (j = i1; (j < i2); j++)
 180                 {
 181                     k = AA[j];
 182                     /*
 183                      * First we must test whether k <> i, and then,
 184                      * because the exclusions are all listed twice i->k
 185                      * and k->i we must select just one of the two.  As
 186                      * a minor optimization we only compute forces when
 187                      * the charges are non-zero.
 188                      */
 189                     if (k > i)
 190                     {
 191                         qqA = qiA*chargeA[k];
 192                         if (EVDW_PME(fr->vdwtype))
 193                         {
 194                             c6A  = c6Ai * C6A[k];
 195                             if (bDoingLBRule)
 196                             {
 197                                 c6A *= pow(0.5*(sigmaA[i]+sigmaA[k]), 6)*sigma3A[k];
 198                             }
 199                         }
 200                         if (qqA != 0.0 || c6A != 0.0)
 201                         {
 202                             real fscal;
 203
 204                             fscal = 0;
 205                             rvec_sub(x[i], x[k], dx);
 206                             if (bMolPBC)
 207                             {
 208                                 /* Cheap pbc_dx, assume excluded pairs are at short distance. */
 209                                 for (m = DIM-1; (m >= 0); m--)
 210                                 {
 211                                     if (dx[m] > 0.5*box[m][m])
 212                                     {
 213                                         rvec_dec(dx, box[m]);
 214                                     }
 215                                     else if (dx[m] < -0.5*box[m][m])
 216                                     {
 217                                         rvec_inc(dx, box[m]);
 218                                     }
 219                                 }
 220                             }
 221                             dr2 = norm2(dx);
 222                             /* Distance between two excluded particles
 223                              * may be zero in the case of shells
 224                              */
 225                             if (dr2 != 0)
 226                             {
 227                                 rinv              = gmx_invsqrt(dr2);
 228                                 rinv2             = rinv*rinv;
 229                                 if (qqA != 0.0)
 230                                 {
 231                                     real dr;
 232
 233                                     dr       = 1.0/rinv;
 234                                     ewcdr    = ewc_q*dr;
 235                                     vc       = qqA*gmx_erf(ewcdr)*rinv;
 236                                     Vexcl_q += vc;
 237 #ifdef GMX_DOUBLE
 238                                     /* Relative accuracy at R_ERF_R_INACC of 3e-10 */
 239 #define       R_ERF_R_INACC 0.006
 240 #else
 241                                     /* Relative accuracy at R_ERF_R_INACC of 2e-5 */
 242 #define       R_ERF_R_INACC 0.1
 243 #endif
 244                                     /* fscal is the scalar force pre-multiplied by rinv,
 245                                      * to normalise the relative position vector dx */
 246                                     if (ewcdr > R_ERF_R_INACC)
 247                                     {
 248                                         fscal = rinv2*(vc - qqA*ewc_q*M_2_SQRTPI*exp(-ewcdr*ewcdr));
 249                                     }
 250                                     else
 251                                     {
 252                                         /* Use a fourth order series expansion for small ewcdr */
 253                                         fscal = ewc_q*ewc_q*qqA*vr0_q*(2.0/3.0 - 0.4*ewcdr*ewcdr);
 254                                     }
 255
 256                                     /* The force vector is obtained by multiplication with
 257                                      * the relative position vector
 258                                      */
 259                                     svmul(fscal, dx, df);
 260                                     rvec_inc(f[k], df);
 261                                     rvec_dec(f[i], df);
 262                                     for (iv = 0; (iv < DIM); iv++)
 263                                     {
 264                                         for (jv = 0; (jv < DIM); jv++)
 265                                         {
 266                                             dxdf_q[iv][jv] += dx[iv]*df[jv];
 267                                         }
 268                                     }
 269                                 }
 270
 271                                 if (c6A != 0.0)
 272                                 {
 273                                     rinv6     = rinv2*rinv2*rinv2;
 274                                     ewcdr2    = ewc_lj2*dr2;
 275                                     ewcdr4    = ewcdr2*ewcdr2;
 276                                     /* We get the excluded long-range contribution from -C6*(1-g(r))
 277                                      * g(r) is also defined in the manual under LJ-PME
 278                                      */
 279                                     vc        = -c6A*rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
 280                                     Vexcl_lj += vc;
 281                                     /* The force is the derivative of the potential vc.
 282                                      * fscal is the scalar force pre-multiplied by rinv,
 283                                      * to normalise the relative position vector dx */
 284                                     fscal     = 6.0*vc*rinv2 + c6A*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
 285
 286                                     /* The force vector is obtained by multiplication with
 287                                      * the relative position vector
 288                                      */
 289                                     svmul(fscal, dx, df);
 290                                     rvec_inc(f[k], df);
 291                                     rvec_dec(f[i], df);
 292                                     for (iv = 0; (iv < DIM); iv++)
 293                                     {
 294                                         for (jv = 0; (jv < DIM); jv++)
 295                                         {
 296                                             dxdf_lj[iv][jv] += dx[iv]*df[jv];
 297                                         }
 298                                     }
 299                                 }
 300                             }
 301                             else
 302                             {
 303                                 Vexcl_q  += qqA*vr0_q;
 304                                 Vexcl_lj += c6A*vr0_lj;
 305                             }
 306                         }
 307                     }
 308                 }
 309             }
 310             /* Dipole correction on force */
 311             if (dipole_coeff != 0)
 312             {
 313                 for (j = 0; (j < DIM); j++)
 314                 {
 315                     f[i][j] -= dipcorrA[j]*chargeA[i];
 316                 }
 317             }
 318         }
 319     }
 320     else if (calc_excl_corr || dipole_coeff != 0)
 321     {
 322         for (i = start; (i < end); i++)
 323         {
 324             /* Initiate local variables (for this i-particle) to 0 */
 325             qiA = chargeA[i]*one_4pi_eps;
 326             qiB = chargeB[i]*one_4pi_eps;
 327             if (EVDW_PME(fr->vdwtype))
 328             {
 329                 c6Ai = C6A[i];
 330                 c6Bi = C6B[i];
 331                 if (bDoingLBRule)
 332                 {
 333                     c6Ai *= sigma3A[i];
 334                     c6Bi *= sigma3B[i];
 335                 }
 336             }
 337             if (calc_excl_corr)
 338             {
 339                 i1  = excl->index[i];
 340                 i2  = excl->index[i+1];
 341
 342                 /* Loop over excluded neighbours */
 343                 for (j = i1; (j < i2); j++)
 344                 {
 345                     k = AA[j];
 346                     if (k > i)
 347                     {
 348                         qqA = qiA*chargeA[k];
 349                         qqB = qiB*chargeB[k];
 350                         if (EVDW_PME(fr->vdwtype))
 351                         {
 352                             c6A = c6Ai*C6A[k];
 353                             c6B = c6Bi*C6B[k];
 354                             if (bDoingLBRule)
 355                             {
 356                                 c6A *= pow(0.5*(sigmaA[i]+sigmaA[k]), 6)*sigma3A[k];
 357                                 c6B *= pow(0.5*(sigmaB[i]+sigmaB[k]), 6)*sigma3B[k];
 358                             }
 359                         }
 360                         if (qqA != 0.0 || qqB != 0.0 || c6A != 0.0 || c6B != 0.0)
 361                         {
 362                             real fscal;
 363
 364                             fscal = 0;
 365                             qqL   = L1_q*qqA + lambda_q*qqB;
 366                             if (EVDW_PME(fr->vdwtype))
 367                             {
 368                                 c6L = L1_lj*c6A + lambda_lj*c6B;
 369                             }
 370                             rvec_sub(x[i], x[k], dx);
 371                             if (bMolPBC)
 372                             {
 373                                 /* Cheap pbc_dx, assume excluded pairs are at short distance. */
 374                                 for (m = DIM-1; (m >= 0); m--)
 375                                 {
 376                                     if (dx[m] > 0.5*box[m][m])
 377                                     {
 378                                         rvec_dec(dx, box[m]);
 379                                     }
 380                                     else if (dx[m] < -0.5*box[m][m])
 381                                     {
 382                                         rvec_inc(dx, box[m]);
 383                                     }
 384                                 }
 385                             }
 386                             dr2 = norm2(dx);
 387                             if (dr2 != 0)
 388                             {
 389                                 rinv    = gmx_invsqrt(dr2);
 390                                 rinv2   = rinv*rinv;
 391                                 if (qqA != 0.0 || qqB != 0.0)
 392                                 {
 393                                     real dr;
 394
 395                                     dr           = 1.0/rinv;
 396                                     v            = gmx_erf(ewc_q*dr)*rinv;
 397                                     vc           = qqL*v;
 398                                     Vexcl_q     += vc;
 399                                     /* fscal is the scalar force pre-multiplied by rinv,
 400                                      * to normalise the relative position vector dx */
 401                                     fscal        = rinv2*(vc-qqL*ewc_q*M_2_SQRTPI*exp(-ewc_q*ewc_q*dr2));
 402                                     dvdl_excl_q += (qqB - qqA)*v;
 403
 404                                     /* The force vector is obtained by multiplication with
 405                                      * the relative position vector
 406                                      */
 407                                     svmul(fscal, dx, df);
 408                                     rvec_inc(f[k], df);
 409                                     rvec_dec(f[i], df);
 410                                     for (iv = 0; (iv < DIM); iv++)
 411                                     {
 412                                         for (jv = 0; (jv < DIM); jv++)
 413                                         {
 414                                             dxdf_q[iv][jv] += dx[iv]*df[jv];
 415                                         }
 416                                     }
 417                                 }
 418
 419                                 if ((c6A != 0.0 || c6B != 0.0) && EVDW_PME(fr->vdwtype))
 420                                 {
 421                                     rinv6         = rinv2*rinv2*rinv2;
 422                                     ewcdr2        = ewc_lj2*dr2;
 423                                     ewcdr4        = ewcdr2*ewcdr2;
 424                                     v             = -rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
 425                                     vc            = c6L*v;
 426                                     Vexcl_lj     += vc;
 427                                     /* fscal is the scalar force pre-multiplied by rinv,
 428                                      * to normalise the relative position vector dx */
 429                                     fscal         = 6.0*vc*rinv2 + c6L*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
 430                                     dvdl_excl_lj += (c6B - c6A)*v;
 431
 432                                     /* The force vector is obtained by multiplication with
 433                                      * the relative position vector
 434                                      */
 435                                     svmul(fscal, dx, df);
 436                                     rvec_inc(f[k], df);
 437                                     rvec_dec(f[i], df);
 438                                     for (iv = 0; (iv < DIM); iv++)
 439                                     {
 440                                         for (jv = 0; (jv < DIM); jv++)
 441                                         {
 442                                             dxdf_lj[iv][jv] += dx[iv]*df[jv];
 443                                         }
 444                                     }
 445                                 }
 446                             }
 447                             else
 448                             {
 449                                 Vexcl_q      += qqL*vr0_q;
 450                                 dvdl_excl_q  += (qqB - qqA)*vr0_q;
 451                                 Vexcl_lj     += c6L*vr0_lj;
 452                                 dvdl_excl_lj += (c6B - c6A)*vr0_lj;
 453                             }
 454                         }
 455                     }
 456                 }
 457             }
 458             /* Dipole correction on force */
 459             if (dipole_coeff != 0)
 460             {
 461                 for (j = 0; (j < DIM); j++)
 462                 {
 463                     f[i][j] -= L1_q*dipcorrA[j]*chargeA[i]
 464                         + lambda_q*dipcorrB[j]*chargeB[i];
 465                 }
 466             }
 467         }
 468     }
 469     for (iv = 0; (iv < DIM); iv++)
 470     {
 471         for (jv = 0; (jv < DIM); jv++)
 472         {
 473             vir_q[iv][jv]  += 0.5*dxdf_q[iv][jv];
 474             vir_lj[iv][jv] += 0.5*dxdf_lj[iv][jv];
 475         }
 476     }
 477
 478     Vself_q[0]  = 0;
 479     Vself_q[1]  = 0;
 480     Vself_lj[0] = 0;
 481     Vself_lj[1] = 0;
 482
 483     /* Global corrections only on master process */
 484     if (MASTER(cr) && thread == 0)
 485     {
 486         for (q = 0; q < (bHaveChargeOrTypePerturbed ? 2 : 1); q++)
 487         {
 488             if (calc_excl_corr)
 489             {
 490                 /* Self-energy correction */
 491                 Vself_q[q] = ewc_q*one_4pi_eps*fr->q2sum[q]*M_1_SQRTPI;
 492                 if (EVDW_PME(fr->vdwtype))
 493                 {
 494                     Vself_lj[q] =  fr->c6sum[q]*0.5*vr0_lj;
 495                 }
 496             }
 497
 498             /* Apply surface dipole correction:
 499              * correction = dipole_coeff * (dipole)^2
 500              */
 501             if (dipole_coeff != 0)
 502             {
 503                 if (ewald_geometry == eewg3D)
 504                 {
 505                     Vdipole[q] = dipole_coeff*iprod(mutot[q], mutot[q]);
 506                 }
 507                 else if (ewald_geometry == eewg3DC)
 508                 {
 509                     Vdipole[q] = dipole_coeff*mutot[q][ZZ]*mutot[q][ZZ];
 510                 }
 511             }
 512         }
 513     }
 514     if (!bHaveChargeOrTypePerturbed)
 515     {
 516         *Vcorr_q = Vdipole[0] - Vself_q[0] - Vexcl_q;
 517         if (EVDW_PME(fr->vdwtype))
 518         {
 519             *Vcorr_lj = -Vself_lj[0] - Vexcl_lj;
 520         }
 521     }
 522     else
 523     {
 524         *Vcorr_q = L1_q*(Vdipole[0] - Vself_q[0])
 525             + lambda_q*(Vdipole[1] - Vself_q[1])
 526             - Vexcl_q;
 527         *dvdlambda_q += Vdipole[1] - Vself_q[1]
 528             - (Vdipole[0] - Vself_q[0]) - dvdl_excl_q;
 529         if (EVDW_PME(fr->vdwtype))
 530         {
 531             *Vcorr_lj      = -(L1_lj*Vself_lj[0] + lambda_lj*Vself_lj[1]) - Vexcl_lj;
 532             *dvdlambda_lj += -Vself_lj[1] + Vself_lj[0] - dvdl_excl_lj;
 533         }
 534     }
 535
 536     if (debug)
 537     {
 538         fprintf(debug, "Long Range corrections for Ewald interactions:\n");
 539         fprintf(debug, "start=%d,natoms=%d\n", start, end-start);
 540         fprintf(debug, "q2sum = %g, Vself_q=%g c6sum = %g, Vself_lj=%g\n",
 541                 L1_q*fr->q2sum[0]+lambda_q*fr->q2sum[1], L1_q*Vself_q[0]+lambda_q*Vself_q[1], L1_lj*fr->c6sum[0]+lambda_lj*fr->c6sum[1], L1_lj*Vself_lj[0]+lambda_lj*Vself_lj[1]);
 542         fprintf(debug, "Electrostatic Long Range correction: Vexcl=%g\n", Vexcl_q);
 543         fprintf(debug, "Lennard-Jones Long Range correction: Vexcl=%g\n", Vexcl_lj);
 544         if (MASTER(cr) && thread == 0)
 545         {
 546             if (epsilon_surface > 0 || ewald_geometry == eewg3DC)
 547             {
 548                 fprintf(debug, "Total dipole correction: Vdipole=%g\n",
 549                         L1_q*Vdipole[0]+lambda_q*Vdipole[1]);
 550             }
 551         }
 552     }
 553 }