src/gromacs/ewald/long-range-correction.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, 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
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  37 #include "gmxpre.h"
  38
  39 #include "long-range-correction.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/math/functions.h"
  44 #include "gromacs/math/units.h"
  45 #include "gromacs/math/utilities.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/mdtypes/commrec.h"
  48 #include "gromacs/mdtypes/forcerec.h"
  49 #include "gromacs/mdtypes/md_enums.h"
  50 #include "gromacs/utility/fatalerror.h"
  51
  52 /* There's nothing special to do here if just masses are perturbed,
  53  * but if either charge or type is perturbed then the implementation
  54  * requires that B states are defined for both charge and type, and
  55  * does not optimize for the cases where only one changes.
  56  *
  57  * The parameter vectors for B states are left undefined in atoms2md()
  58  * when either FEP is inactive, or when there are no mass/charge/type
  59  * perturbations. The parameter vectors for LJ-PME are likewise
  60  * undefined when LJ-PME is not active. This works because
  61  * bHaveChargeOrTypePerturbed handles the control flow. */
  62 void ewald_LRcorrection(int start, int end,
  63                         t_commrec *cr, int thread, t_forcerec *fr,
  64                         real *chargeA, real *chargeB,
  65                         real *C6A, real *C6B,
  66                         real *sigmaA, real *sigmaB,
  67                         real *sigma3A, real *sigma3B,
  68                         gmx_bool bHaveChargeOrTypePerturbed,
  69                         gmx_bool calc_excl_corr,
  70                         t_blocka *excl, rvec x[],
  71                         matrix box, rvec mu_tot[],
  72                         int ewald_geometry, real epsilon_surface,
  73                         rvec *f, tensor vir_q, tensor vir_lj,
  74                         real *Vcorr_q, real *Vcorr_lj,
  75                         real lambda_q, real lambda_lj,
  76                         real *dvdlambda_q, real *dvdlambda_lj)
  77 {
  78     int         i, i1, i2, j, k, m, iv, jv, q;
  79     int        *AA;
  80     double      Vexcl_q, dvdl_excl_q, dvdl_excl_lj; /* Necessary for precision */
  81     double      Vexcl_lj;
  82     real        one_4pi_eps;
  83     real        v, vc, qiA, qiB, dr2, rinv;
  84     real        Vself_q[2], Vself_lj[2], Vdipole[2], rinv2, ewc_q = fr->ewaldcoeff_q, ewcdr;
  85     real        ewc_lj = fr->ewaldcoeff_lj, ewc_lj2 = ewc_lj * ewc_lj;
  86     real        c6Ai   = 0, c6Bi = 0, c6A = 0, c6B = 0, ewcdr2, ewcdr4, c6L = 0, rinv6;
  87     rvec        df, dx, mutot[2], dipcorrA, dipcorrB;
  88     tensor      dxdf_q = {{0}}, dxdf_lj = {{0}};
  89     real        vol    = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
  90     real        L1_q, L1_lj, dipole_coeff, qqA, qqB, qqL, vr0_q, vr0_lj = 0;
  91     gmx_bool    bMolPBC      = fr->bMolPBC;
  92     gmx_bool    bDoingLBRule = (fr->ljpme_combination_rule == eljpmeLB);
  93     gmx_bool    bNeedLongRangeCorrection;
  94
  95     /* This routine can be made faster by using tables instead of analytical interactions
  96      * However, that requires a thorough verification that they are correct in all cases.
  97      */
  98
  99     one_4pi_eps   = ONE_4PI_EPS0/fr->epsilon_r;
 100     vr0_q         = ewc_q*M_2_SQRTPI;
 101     if (EVDW_PME(fr->vdwtype))
 102     {
 103         vr0_lj    = -gmx::power6(ewc_lj)/6.0;
 104     }
 105
 106     AA           = excl->a;
 107     Vexcl_q      = 0;
 108     Vexcl_lj     = 0;
 109     dvdl_excl_q  = 0;
 110     dvdl_excl_lj = 0;
 111     Vdipole[0]   = 0;
 112     Vdipole[1]   = 0;
 113     L1_q         = 1.0-lambda_q;
 114     L1_lj        = 1.0-lambda_lj;
 115     /* Note that we have to transform back to gromacs units, since
 116      * mu_tot contains the dipole in debye units (for output).
 117      */
 118     for (i = 0; (i < DIM); i++)
 119     {
 120         mutot[0][i] = mu_tot[0][i]*DEBYE2ENM;
 121         mutot[1][i] = mu_tot[1][i]*DEBYE2ENM;
 122         dipcorrA[i] = 0;
 123         dipcorrB[i] = 0;
 124     }
 125     dipole_coeff = 0;
 126     switch (ewald_geometry)
 127     {
 128         case eewg3D:
 129             if (epsilon_surface != 0)
 130             {
 131                 dipole_coeff =
 132                     2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + fr->epsilon_r)*vol);
 133                 for (i = 0; (i < DIM); i++)
 134                 {
 135                     dipcorrA[i] = 2*dipole_coeff*mutot[0][i];
 136                     dipcorrB[i] = 2*dipole_coeff*mutot[1][i];
 137                 }
 138             }
 139             break;
 140         case eewg3DC:
 141             dipole_coeff = 2*M_PI*one_4pi_eps/vol;
 142             dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
 143             dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
 144             break;
 145         default:
 146             gmx_incons("Unsupported Ewald geometry");
 147             break;
 148     }
 149     if (debug)
 150     {
 151         fprintf(debug, "dipcorr = %8.3f  %8.3f  %8.3f\n",
 152                 dipcorrA[XX], dipcorrA[YY], dipcorrA[ZZ]);
 153         fprintf(debug, "mutot   = %8.3f  %8.3f  %8.3f\n",
 154                 mutot[0][XX], mutot[0][YY], mutot[0][ZZ]);
 155     }
 156     bNeedLongRangeCorrection = (calc_excl_corr || dipole_coeff != 0);
 157     if (bNeedLongRangeCorrection && !bHaveChargeOrTypePerturbed)
 158     {
 159         for (i = start; (i < end); i++)
 160         {
 161             /* Initiate local variables (for this i-particle) to 0 */
 162             qiA = chargeA[i]*one_4pi_eps;
 163             if (EVDW_PME(fr->vdwtype))
 164             {
 165                 c6Ai = C6A[i];
 166                 if (bDoingLBRule)
 167                 {
 168                     c6Ai *= sigma3A[i];
 169                 }
 170             }
 171             if (calc_excl_corr)
 172             {
 173                 i1  = excl->index[i];
 174                 i2  = excl->index[i+1];
 175
 176                 /* Loop over excluded neighbours */
 177                 for (j = i1; (j < i2); j++)
 178                 {
 179                     k = AA[j];
 180                     /*
 181                      * First we must test whether k <> i, and then,
 182                      * because the exclusions are all listed twice i->k
 183                      * and k->i we must select just one of the two.  As
 184                      * a minor optimization we only compute forces when
 185                      * the charges are non-zero.
 186                      */
 187                     if (k > i)
 188                     {
 189                         qqA = qiA*chargeA[k];
 190                         if (EVDW_PME(fr->vdwtype))
 191                         {
 192                             c6A  = c6Ai * C6A[k];
 193                             if (bDoingLBRule)
 194                             {
 195                                 c6A *= gmx::power6(0.5*(sigmaA[i]+sigmaA[k]))*sigma3A[k];
 196                             }
 197                         }
 198                         if (qqA != 0.0 || c6A != 0.0)
 199                         {
 200                             rvec_sub(x[i], x[k], dx);
 201                             if (bMolPBC)
 202                             {
 203                                 /* Cheap pbc_dx, assume excluded pairs are at short distance. */
 204                                 for (m = DIM-1; (m >= 0); m--)
 205                                 {
 206                                     if (dx[m] > 0.5*box[m][m])
 207                                     {
 208                                         rvec_dec(dx, box[m]);
 209                                     }
 210                                     else if (dx[m] < -0.5*box[m][m])
 211                                     {
 212                                         rvec_inc(dx, box[m]);
 213                                     }
 214                                 }
 215                             }
 216                             dr2 = norm2(dx);
 217                             /* Distance between two excluded particles
 218                              * may be zero in the case of shells
 219                              */
 220                             if (dr2 != 0)
 221                             {
 222                                 rinv              = gmx::invsqrt(dr2);
 223                                 rinv2             = rinv*rinv;
 224                                 if (qqA != 0.0)
 225                                 {
 226                                     real dr, fscal;
 227
 228                                     dr       = 1.0/rinv;
 229                                     ewcdr    = ewc_q*dr;
 230                                     vc       = qqA*std::erf(ewcdr)*rinv;
 231                                     Vexcl_q += vc;
 232 #if GMX_DOUBLE
 233                                     /* Relative accuracy at R_ERF_R_INACC of 3e-10 */
 234 #define       R_ERF_R_INACC 0.006
 235 #else
 236                                     /* Relative accuracy at R_ERF_R_INACC of 2e-5 */
 237 #define       R_ERF_R_INACC 0.1
 238 #endif
 239                                     /* fscal is the scalar force pre-multiplied by rinv,
 240                                      * to normalise the relative position vector dx */
 241                                     if (ewcdr > R_ERF_R_INACC)
 242                                     {
 243                                         fscal = rinv2*(vc - qqA*ewc_q*M_2_SQRTPI*exp(-ewcdr*ewcdr));
 244                                     }
 245                                     else
 246                                     {
 247                                         /* Use a fourth order series expansion for small ewcdr */
 248                                         fscal = ewc_q*ewc_q*qqA*vr0_q*(2.0/3.0 - 0.4*ewcdr*ewcdr);
 249                                     }
 250
 251                                     /* The force vector is obtained by multiplication with
 252                                      * the relative position vector
 253                                      */
 254                                     svmul(fscal, dx, df);
 255                                     rvec_inc(f[k], df);
 256                                     rvec_dec(f[i], df);
 257                                     for (iv = 0; (iv < DIM); iv++)
 258                                     {
 259                                         for (jv = 0; (jv < DIM); jv++)
 260                                         {
 261                                             dxdf_q[iv][jv] += dx[iv]*df[jv];
 262                                         }
 263                                     }
 264                                 }
 265
 266                                 if (c6A != 0.0)
 267                                 {
 268                                     real fscal;
 269
 270                                     rinv6     = rinv2*rinv2*rinv2;
 271                                     ewcdr2    = ewc_lj2*dr2;
 272                                     ewcdr4    = ewcdr2*ewcdr2;
 273                                     /* We get the excluded long-range contribution from -C6*(1-g(r))
 274                                      * g(r) is also defined in the manual under LJ-PME
 275                                      */
 276                                     vc        = -c6A*rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
 277                                     Vexcl_lj += vc;
 278                                     /* The force is the derivative of the potential vc.
 279                                      * fscal is the scalar force pre-multiplied by rinv,
 280                                      * to normalise the relative position vector dx */
 281                                     fscal     = 6.0*vc*rinv2 + c6A*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
 282
 283                                     /* The force vector is obtained by multiplication with
 284                                      * the relative position vector
 285                                      */
 286                                     svmul(fscal, dx, df);
 287                                     rvec_inc(f[k], df);
 288                                     rvec_dec(f[i], df);
 289                                     for (iv = 0; (iv < DIM); iv++)
 290                                     {
 291                                         for (jv = 0; (jv < DIM); jv++)
 292                                         {
 293                                             dxdf_lj[iv][jv] += dx[iv]*df[jv];
 294                                         }
 295                                     }
 296                                 }
 297                             }
 298                             else
 299                             {
 300                                 Vexcl_q  += qqA*vr0_q;
 301                                 Vexcl_lj += c6A*vr0_lj;
 302                             }
 303                         }
 304                     }
 305                 }
 306             }
 307             /* Dipole correction on force */
 308             if (dipole_coeff != 0)
 309             {
 310                 for (j = 0; (j < DIM); j++)
 311                 {
 312                     f[i][j] -= dipcorrA[j]*chargeA[i];
 313                 }
 314             }
 315         }
 316     }
 317     else if (bNeedLongRangeCorrection)
 318     {
 319         for (i = start; (i < end); i++)
 320         {
 321             /* Initiate local variables (for this i-particle) to 0 */
 322             qiA = chargeA[i]*one_4pi_eps;
 323             qiB = chargeB[i]*one_4pi_eps;
 324             if (EVDW_PME(fr->vdwtype))
 325             {
 326                 c6Ai = C6A[i];
 327                 c6Bi = C6B[i];
 328                 if (bDoingLBRule)
 329                 {
 330                     c6Ai *= sigma3A[i];
 331                     c6Bi *= sigma3B[i];
 332                 }
 333             }
 334             if (calc_excl_corr)
 335             {
 336                 i1  = excl->index[i];
 337                 i2  = excl->index[i+1];
 338
 339                 /* Loop over excluded neighbours */
 340                 for (j = i1; (j < i2); j++)
 341                 {
 342                     k = AA[j];
 343                     if (k > i)
 344                     {
 345                         qqA = qiA*chargeA[k];
 346                         qqB = qiB*chargeB[k];
 347                         if (EVDW_PME(fr->vdwtype))
 348                         {
 349                             c6A = c6Ai*C6A[k];
 350                             c6B = c6Bi*C6B[k];
 351                             if (bDoingLBRule)
 352                             {
 353                                 c6A *= gmx::power6(0.5*(sigmaA[i]+sigmaA[k]))*sigma3A[k];
 354                                 c6B *= gmx::power6(0.5*(sigmaB[i]+sigmaB[k]))*sigma3B[k];
 355                             }
 356                         }
 357                         if (qqA != 0.0 || qqB != 0.0 || c6A != 0.0 || c6B != 0.0)
 358                         {
 359                             real fscal;
 360
 361                             qqL   = L1_q*qqA + lambda_q*qqB;
 362                             if (EVDW_PME(fr->vdwtype))
 363                             {
 364                                 c6L = L1_lj*c6A + lambda_lj*c6B;
 365                             }
 366                             rvec_sub(x[i], x[k], dx);
 367                             if (bMolPBC)
 368                             {
 369                                 /* Cheap pbc_dx, assume excluded pairs are at short distance. */
 370                                 for (m = DIM-1; (m >= 0); m--)
 371                                 {
 372                                     if (dx[m] > 0.5*box[m][m])
 373                                     {
 374                                         rvec_dec(dx, box[m]);
 375                                     }
 376                                     else if (dx[m] < -0.5*box[m][m])
 377                                     {
 378                                         rvec_inc(dx, box[m]);
 379                                     }
 380                                 }
 381                             }
 382                             dr2 = norm2(dx);
 383                             if (dr2 != 0)
 384                             {
 385                                 rinv    = gmx::invsqrt(dr2);
 386                                 rinv2   = rinv*rinv;
 387                                 if (qqA != 0.0 || qqB != 0.0)
 388                                 {
 389                                     real dr;
 390
 391                                     dr           = 1.0/rinv;
 392                                     v            = std::erf(ewc_q*dr)*rinv;
 393                                     vc           = qqL*v;
 394                                     Vexcl_q     += vc;
 395                                     /* fscal is the scalar force pre-multiplied by rinv,
 396                                      * to normalise the relative position vector dx */
 397                                     fscal        = rinv2*(vc-qqL*ewc_q*M_2_SQRTPI*exp(-ewc_q*ewc_q*dr2));
 398                                     dvdl_excl_q += (qqB - qqA)*v;
 399
 400                                     /* The force vector is obtained by multiplication with
 401                                      * the relative position vector
 402                                      */
 403                                     svmul(fscal, dx, df);
 404                                     rvec_inc(f[k], df);
 405                                     rvec_dec(f[i], df);
 406                                     for (iv = 0; (iv < DIM); iv++)
 407                                     {
 408                                         for (jv = 0; (jv < DIM); jv++)
 409                                         {
 410                                             dxdf_q[iv][jv] += dx[iv]*df[jv];
 411                                         }
 412                                     }
 413                                 }
 414
 415                                 if ((c6A != 0.0 || c6B != 0.0) && EVDW_PME(fr->vdwtype))
 416                                 {
 417                                     rinv6         = rinv2*rinv2*rinv2;
 418                                     ewcdr2        = ewc_lj2*dr2;
 419                                     ewcdr4        = ewcdr2*ewcdr2;
 420                                     v             = -rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
 421                                     vc            = c6L*v;
 422                                     Vexcl_lj     += vc;
 423                                     /* fscal is the scalar force pre-multiplied by rinv,
 424                                      * to normalise the relative position vector dx */
 425                                     fscal         = 6.0*vc*rinv2 + c6L*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
 426                                     dvdl_excl_lj += (c6B - c6A)*v;
 427
 428                                     /* The force vector is obtained by multiplication with
 429                                      * the relative position vector
 430                                      */
 431                                     svmul(fscal, dx, df);
 432                                     rvec_inc(f[k], df);
 433                                     rvec_dec(f[i], df);
 434                                     for (iv = 0; (iv < DIM); iv++)
 435                                     {
 436                                         for (jv = 0; (jv < DIM); jv++)
 437                                         {
 438                                             dxdf_lj[iv][jv] += dx[iv]*df[jv];
 439                                         }
 440                                     }
 441                                 }
 442                             }
 443                             else
 444                             {
 445                                 Vexcl_q      += qqL*vr0_q;
 446                                 dvdl_excl_q  += (qqB - qqA)*vr0_q;
 447                                 Vexcl_lj     += c6L*vr0_lj;
 448                                 dvdl_excl_lj += (c6B - c6A)*vr0_lj;
 449                             }
 450                         }
 451                     }
 452                 }
 453             }
 454             /* Dipole correction on force */
 455             if (dipole_coeff != 0)
 456             {
 457                 for (j = 0; (j < DIM); j++)
 458                 {
 459                     f[i][j] -= L1_q*dipcorrA[j]*chargeA[i]
 460                         + lambda_q*dipcorrB[j]*chargeB[i];
 461                 }
 462             }
 463         }
 464     }
 465     for (iv = 0; (iv < DIM); iv++)
 466     {
 467         for (jv = 0; (jv < DIM); jv++)
 468         {
 469             vir_q[iv][jv]  += 0.5*dxdf_q[iv][jv];
 470             vir_lj[iv][jv] += 0.5*dxdf_lj[iv][jv];
 471         }
 472     }
 473
 474     Vself_q[0]  = 0;
 475     Vself_q[1]  = 0;
 476     Vself_lj[0] = 0;
 477     Vself_lj[1] = 0;
 478
 479     /* Global corrections only on master process */
 480     if (MASTER(cr) && thread == 0)
 481     {
 482         for (q = 0; q < (bHaveChargeOrTypePerturbed ? 2 : 1); q++)
 483         {
 484             if (calc_excl_corr)
 485             {
 486                 /* Self-energy correction */
 487                 Vself_q[q] = ewc_q*one_4pi_eps*fr->q2sum[q]*M_1_SQRTPI;
 488                 if (EVDW_PME(fr->vdwtype))
 489                 {
 490                     Vself_lj[q] =  fr->c6sum[q]*0.5*vr0_lj;
 491                 }
 492             }
 493
 494             /* Apply surface dipole correction:
 495              * correction = dipole_coeff * (dipole)^2
 496              */
 497             if (dipole_coeff != 0)
 498             {
 499                 if (ewald_geometry == eewg3D)
 500                 {
 501                     Vdipole[q] = dipole_coeff*iprod(mutot[q], mutot[q]);
 502                 }
 503                 else if (ewald_geometry == eewg3DC)
 504                 {
 505                     Vdipole[q] = dipole_coeff*mutot[q][ZZ]*mutot[q][ZZ];
 506                 }
 507             }
 508         }
 509     }
 510     if (!bHaveChargeOrTypePerturbed)
 511     {
 512         *Vcorr_q = Vdipole[0] - Vself_q[0] - Vexcl_q;
 513         if (EVDW_PME(fr->vdwtype))
 514         {
 515             *Vcorr_lj = -Vself_lj[0] - Vexcl_lj;
 516         }
 517     }
 518     else
 519     {
 520         *Vcorr_q = L1_q*(Vdipole[0] - Vself_q[0])
 521             + lambda_q*(Vdipole[1] - Vself_q[1])
 522             - Vexcl_q;
 523         *dvdlambda_q += Vdipole[1] - Vself_q[1]
 524             - (Vdipole[0] - Vself_q[0]) - dvdl_excl_q;
 525         if (EVDW_PME(fr->vdwtype))
 526         {
 527             *Vcorr_lj      = -(L1_lj*Vself_lj[0] + lambda_lj*Vself_lj[1]) - Vexcl_lj;
 528             *dvdlambda_lj += -Vself_lj[1] + Vself_lj[0] - dvdl_excl_lj;
 529         }
 530     }
 531
 532     if (debug)
 533     {
 534         fprintf(debug, "Long Range corrections for Ewald interactions:\n");
 535         fprintf(debug, "start=%d,natoms=%d\n", start, end-start);
 536         fprintf(debug, "q2sum = %g, Vself_q=%g c6sum = %g, Vself_lj=%g\n",
 537                 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]);
 538         fprintf(debug, "Electrostatic Long Range correction: Vexcl=%g\n", Vexcl_q);
 539         fprintf(debug, "Lennard-Jones Long Range correction: Vexcl=%g\n", Vexcl_lj);
 540         if (MASTER(cr) && thread == 0)
 541         {
 542             if (epsilon_surface > 0 || ewald_geometry == eewg3DC)
 543             {
 544                 fprintf(debug, "Total dipole correction: Vdipole=%g\n",
 545                         L1_q*Vdipole[0]+lambda_q*Vdipole[1]);
 546             }
 547         }
 548     }
 549 }