src/gromacs/listed_forces/pairs.cpp

   1 /*
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   5  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
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  36 /*! \internal \file
  37  *
  38  * \brief This file defines functions for "pair" interactions
  39  * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
  40  *
  41  * \author Mark Abraham <mark.j.abraham@gmail.com>
  42  *
  43  * \ingroup module_listed_forces
  44  */
  45 #include "gmxpre.h"
  46
  47 #include "pairs.h"
  48
  49 #include <cmath>
  50
  51 #include "gromacs/listed_forces/bonded.h"
  52 #include "gromacs/math/functions.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/mdtypes/forcerec.h"
  55 #include "gromacs/mdtypes/group.h"
  56 #include "gromacs/mdtypes/interaction_const.h"
  57 #include "gromacs/mdtypes/md_enums.h"
  58 #include "gromacs/mdtypes/mdatom.h"
  59 #include "gromacs/mdtypes/nblist.h"
  60 #include "gromacs/mdtypes/simulation_workload.h"
  61 #include "gromacs/pbcutil/ishift.h"
  62 #include "gromacs/pbcutil/pbc.h"
  63 #include "gromacs/pbcutil/pbc_simd.h"
  64 #include "gromacs/simd/simd.h"
  65 #include "gromacs/simd/simd_math.h"
  66 #include "gromacs/simd/vector_operations.h"
  67 #include "gromacs/tables/forcetable.h"
  68 #include "gromacs/utility/basedefinitions.h"
  69 #include "gromacs/utility/fatalerror.h"
  70 #include "gromacs/utility/gmxassert.h"
  71
  72 #include "listed_internal.h"
  73
  74 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
  75
  76 /*! \brief Issue a warning if a listed interaction is beyond a table limit */
  77 static void warning_rlimit(const rvec* x, int ai, int aj, int* global_atom_index, real r, real rlimit)
  78 {
  79     gmx_warning(
  80             "Listed nonbonded interaction between particles %d and %d\n"
  81             "at distance %.3f which is larger than the table limit %.3f nm.\n\n"
  82             "This is likely either a 1,4 interaction, or a listed interaction inside\n"
  83             "a smaller molecule you are decoupling during a free energy calculation.\n"
  84             "Since interactions at distances beyond the table cannot be computed,\n"
  85             "they are skipped until they are inside the table limit again. You will\n"
  86             "only see this message once, even if it occurs for several interactions.\n\n"
  87             "IMPORTANT: This should not happen in a stable simulation, so there is\n"
  88             "probably something wrong with your system. Only change the table-extension\n"
  89             "distance in the mdp file if you are really sure that is the reason.\n",
  90             glatnr(global_atom_index, ai),
  91             glatnr(global_atom_index, aj),
  92             r,
  93             rlimit);
  94
  95     if (debug)
  96     {
  97         fprintf(debug,
  98                 "%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. "
  99                 "Ignored\n",
 100                 x[ai][XX],
 101                 x[ai][YY],
 102                 x[ai][ZZ],
 103                 x[aj][XX],
 104                 x[aj][YY],
 105                 x[aj][ZZ],
 106                 glatnr(global_atom_index, ai),
 107                 glatnr(global_atom_index, aj),
 108                 r);
 109     }
 110 }
 111
 112 /*! \brief Compute the energy and force for a single pair interaction */
 113 static real evaluate_single(real        r2,
 114                             real        tabscale,
 115                             const real* vftab,
 116                             real        tableStride,
 117                             real        qq,
 118                             real        c6,
 119                             real        c12,
 120                             real*       velec,
 121                             real*       vvdw)
 122 {
 123     real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
 124     int  ntab;
 125
 126     /* Do the tabulated interactions - first table lookup */
 127     rinv = gmx::invsqrt(r2);
 128     r    = r2 * rinv;
 129     rtab = r * tabscale;
 130     ntab = static_cast<int>(rtab);
 131     eps  = rtab - ntab;
 132     eps2 = eps * eps;
 133     ntab = static_cast<int>(tableStride * ntab);
 134     /* Electrostatics */
 135     Y     = vftab[ntab];
 136     F     = vftab[ntab + 1];
 137     Geps  = eps * vftab[ntab + 2];
 138     Heps2 = eps2 * vftab[ntab + 3];
 139     Fp    = F + Geps + Heps2;
 140     VVe   = Y + eps * Fp;
 141     FFe   = Fp + Geps + 2.0 * Heps2;
 142     /* Dispersion */
 143     Y     = vftab[ntab + 4];
 144     F     = vftab[ntab + 5];
 145     Geps  = eps * vftab[ntab + 6];
 146     Heps2 = eps2 * vftab[ntab + 7];
 147     Fp    = F + Geps + Heps2;
 148     VVd   = Y + eps * Fp;
 149     FFd   = Fp + Geps + 2.0 * Heps2;
 150     /* Repulsion */
 151     Y     = vftab[ntab + 8];
 152     F     = vftab[ntab + 9];
 153     Geps  = eps * vftab[ntab + 10];
 154     Heps2 = eps2 * vftab[ntab + 11];
 155     Fp    = F + Geps + Heps2;
 156     VVr   = Y + eps * Fp;
 157     FFr   = Fp + Geps + 2.0 * Heps2;
 158
 159     *velec = qq * VVe;
 160     *vvdw  = c6 * VVd + c12 * VVr;
 161
 162     fscal = -(qq * FFe + c6 * FFd + c12 * FFr) * tabscale * rinv;
 163
 164     return fscal;
 165 }
 166
 167 static inline real sixthRoot(const real r)
 168 {
 169     return gmx::invsqrt(std::cbrt(r));
 170 }
 171
 172 /*! \brief Compute the energy and force for a single pair interaction under FEP */
 173 static real free_energy_evaluate_single(real                                           r2,
 174                                         const interaction_const_t::SoftCoreParameters& scParams,
 175                                         real                                           tabscale,
 176                                         const real*                                    vftab,
 177                                         real                                           tableStride,
 178                                         real                                           qqA,
 179                                         real                                           c6A,
 180                                         real                                           c12A,
 181                                         real                                           qqB,
 182                                         real                                           c6B,
 183                                         real                                           c12B,
 184                                         const real                                     LFC[2],
 185                                         const real                                     LFV[2],
 186                                         const real                                     DLF[2],
 187                                         const real                                     lfac_coul[2],
 188                                         const real                                     lfac_vdw[2],
 189                                         const real dlfac_coul[2],
 190                                         const real dlfac_vdw[2],
 191                                         real*      velectot,
 192                                         real*      vvdwtot,
 193                                         real*      dvdl)
 194 {
 195     real       rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
 196     real       qq[2], c6[2], c12[2], sigma6[2], sigma_pow[2];
 197     real       alpha_coul_eff, alpha_vdw_eff, dvdl_coul, dvdl_vdw;
 198     real       rpinv, r_coul, r_vdw, velecsum, vvdwsum;
 199     real       fscal_vdw[2], fscal_elec[2];
 200     real       velec[2], vvdw[2];
 201     int        i, ntab;
 202     const real half = 0.5_real;
 203     const real one  = 1.0_real;
 204     const real two  = 2.0_real;
 205
 206     qq[0]  = qqA;
 207     qq[1]  = qqB;
 208     c6[0]  = c6A;
 209     c6[1]  = c6B;
 210     c12[0] = c12A;
 211     c12[1] = c12B;
 212
 213     const real rpm2 = r2 * r2;   /* r4 */
 214     const real rp   = rpm2 * r2; /* r6 */
 215
 216     /* Loop over state A(0) and B(1) */
 217     for (i = 0; i < 2; i++)
 218     {
 219         if ((c6[i] > 0) && (c12[i] > 0))
 220         {
 221             /* The c6 & c12 coefficients now contain the constants 6.0 and 12.0, respectively.
 222              * Correct for this by multiplying with (1/12.0)/(1/6.0)=6.0/12.0=0.5.
 223              */
 224             sigma6[i] = half * c12[i] / c6[i];
 225             if (sigma6[i] < scParams.sigma6Minimum) /* for disappearing coul and vdw with soft core at the same time */
 226             {
 227                 sigma6[i] = scParams.sigma6Minimum;
 228             }
 229         }
 230         else
 231         {
 232             sigma6[i] = scParams.sigma6WithInvalidSigma;
 233         }
 234         sigma_pow[i] = sigma6[i];
 235     }
 236
 237     /* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
 238     if ((c12[0] > 0) && (c12[1] > 0))
 239     {
 240         alpha_vdw_eff  = 0;
 241         alpha_coul_eff = 0;
 242     }
 243     else
 244     {
 245         alpha_vdw_eff  = scParams.alphaVdw;
 246         alpha_coul_eff = scParams.alphaCoulomb;
 247     }
 248
 249     /* Loop over A and B states again */
 250     for (i = 0; i < 2; i++)
 251     {
 252         fscal_elec[i] = 0;
 253         fscal_vdw[i]  = 0;
 254         velec[i]      = 0;
 255         vvdw[i]       = 0;
 256
 257         /* Only spend time on A or B state if it is non-zero */
 258         if ((qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0))
 259         {
 260             /* Coulomb */
 261             rpinv  = one / (alpha_coul_eff * lfac_coul[i] * sigma_pow[i] + rp);
 262             r_coul = sixthRoot(rpinv);
 263
 264             /* Electrostatics table lookup data */
 265             rtab = r_coul * tabscale;
 266             ntab = static_cast<int>(rtab);
 267             eps  = rtab - ntab;
 268             eps2 = eps * eps;
 269             ntab = static_cast<int>(tableStride * ntab);
 270             /* Electrostatics */
 271             Y             = vftab[ntab];
 272             F             = vftab[ntab + 1];
 273             Geps          = eps * vftab[ntab + 2];
 274             Heps2         = eps2 * vftab[ntab + 3];
 275             Fp            = F + Geps + Heps2;
 276             VV            = Y + eps * Fp;
 277             FF            = Fp + Geps + two * Heps2;
 278             velec[i]      = qq[i] * VV;
 279             fscal_elec[i] = -qq[i] * FF * r_coul * rpinv * tabscale;
 280
 281             /* Vdw */
 282             rpinv = one / (alpha_vdw_eff * lfac_vdw[i] * sigma_pow[i] + rp);
 283             r_vdw = sixthRoot(rpinv);
 284             /* Vdw table lookup data */
 285             rtab = r_vdw * tabscale;
 286             ntab = static_cast<int>(rtab);
 287             eps  = rtab - ntab;
 288             eps2 = eps * eps;
 289             ntab = 12 * ntab;
 290             /* Dispersion */
 291             Y            = vftab[ntab + 4];
 292             F            = vftab[ntab + 5];
 293             Geps         = eps * vftab[ntab + 6];
 294             Heps2        = eps2 * vftab[ntab + 7];
 295             Fp           = F + Geps + Heps2;
 296             VV           = Y + eps * Fp;
 297             FF           = Fp + Geps + two * Heps2;
 298             vvdw[i]      = c6[i] * VV;
 299             fscal_vdw[i] = -c6[i] * FF;
 300
 301             /* Repulsion */
 302             Y     = vftab[ntab + 8];
 303             F     = vftab[ntab + 9];
 304             Geps  = eps * vftab[ntab + 10];
 305             Heps2 = eps2 * vftab[ntab + 11];
 306             Fp    = F + Geps + Heps2;
 307             VV    = Y + eps * Fp;
 308             FF    = Fp + Geps + two * Heps2;
 309             vvdw[i] += c12[i] * VV;
 310             fscal_vdw[i] -= c12[i] * FF;
 311             fscal_vdw[i] *= r_vdw * rpinv * tabscale;
 312         }
 313     }
 314     /* Now we have velec[i], vvdw[i], and fscal[i] for both states */
 315     /* Assemble A and B states */
 316     velecsum  = 0;
 317     vvdwsum   = 0;
 318     dvdl_coul = 0;
 319     dvdl_vdw  = 0;
 320     fscal     = 0;
 321     for (i = 0; i < 2; i++)
 322     {
 323         velecsum += LFC[i] * velec[i];
 324         vvdwsum += LFV[i] * vvdw[i];
 325
 326         fscal += (LFC[i] * fscal_elec[i] + LFV[i] * fscal_vdw[i]) * rpm2;
 327
 328         dvdl_coul += velec[i] * DLF[i]
 329                      + LFC[i] * alpha_coul_eff * dlfac_coul[i] * fscal_elec[i] * sigma_pow[i];
 330         dvdl_vdw += vvdw[i] * DLF[i]
 331                     + LFV[i] * alpha_vdw_eff * dlfac_vdw[i] * fscal_vdw[i] * sigma_pow[i];
 332     }
 333
 334     dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)] += dvdl_coul;
 335     dvdl[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)] += dvdl_vdw;
 336
 337     *velectot = velecsum;
 338     *vvdwtot  = vvdwsum;
 339
 340     return fscal;
 341 }
 342
 343 /*! \brief Calculate pair interactions, supports all types and conditions. */
 344 template<BondedKernelFlavor flavor>
 345 static real do_pairs_general(int                 ftype,
 346                              int                 nbonds,
 347                              const t_iatom       iatoms[],
 348                              const t_iparams     iparams[],
 349                              const rvec          x[],
 350                              rvec4               f[],
 351                              rvec                fshift[],
 352                              const struct t_pbc* pbc,
 353                              const real*         lambda,
 354                              real*               dvdl,
 355                              const t_mdatoms*    md,
 356                              const t_forcerec*   fr,
 357                              gmx_grppairener_t*  grppener,
 358                              int*                global_atom_index)
 359 {
 360     real            qq, c6, c12;
 361     rvec            dx;
 362     int             i, itype, ai, aj, gid;
 363     int             fshift_index;
 364     real            r2;
 365     real            fscal, velec, vvdw;
 366     real*           energygrp_elec;
 367     real*           energygrp_vdw;
 368     static gmx_bool warned_rlimit = FALSE;
 369     /* Free energy stuff */
 370     gmx_bool   bFreeEnergy;
 371     real       LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
 372     real       qqB, c6B, c12B;
 373     const real oneSixth = 1.0_real / 6.0_real;
 374
 375     switch (ftype)
 376     {
 377         case F_LJ14:
 378         case F_LJC14_Q:
 379             energygrp_elec = grppener->energyGroupPairTerms[NonBondedEnergyTerms::Coulomb14].data();
 380             energygrp_vdw  = grppener->energyGroupPairTerms[NonBondedEnergyTerms::LJ14].data();
 381             break;
 382         case F_LJC_PAIRS_NB:
 383             energygrp_elec = grppener->energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data();
 384             energygrp_vdw  = grppener->energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data();
 385             break;
 386         default:
 387             energygrp_elec = nullptr; /* Keep compiler happy */
 388             energygrp_vdw  = nullptr; /* Keep compiler happy */
 389             gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
 390     }
 391
 392     if (fr->efep != FreeEnergyPerturbationType::No)
 393     {
 394         /* Lambda factor for state A=1-lambda and B=lambda */
 395         LFC[0] = 1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)];
 396         LFV[0] = 1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)];
 397         LFC[1] = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)];
 398         LFV[1] = lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)];
 399
 400         /*derivative of the lambda factor for state A and B */
 401         DLF[0] = -1;
 402         DLF[1] = 1;
 403
 404         GMX_ASSERT(fr->ic->softCoreParameters, "We need soft-core parameters");
 405         const auto& scParams = *fr->ic->softCoreParameters;
 406
 407         for (i = 0; i < 2; i++)
 408         {
 409             lfac_coul[i] = (scParams.lambdaPower == 2 ? (1 - LFC[i]) * (1 - LFC[i]) : (1 - LFC[i]));
 410             dlfac_coul[i] = DLF[i] * scParams.lambdaPower * oneSixth
 411                             * (scParams.lambdaPower == 2 ? (1 - LFC[i]) : 1);
 412             lfac_vdw[i]  = (scParams.lambdaPower == 2 ? (1 - LFV[i]) * (1 - LFV[i]) : (1 - LFV[i]));
 413             dlfac_vdw[i] = DLF[i] * scParams.lambdaPower * oneSixth
 414                            * (scParams.lambdaPower == 2 ? (1 - LFV[i]) : 1);
 415         }
 416     }
 417
 418     /* TODO This code depends on the logic in tables.c that constructs
 419        the table layout, which should be made explicit in future
 420        cleanup. */
 421     GMX_ASSERT(
 422             etiNR == 3,
 423             "Pair-interaction code that uses GROMACS interaction tables supports exactly 3 tables");
 424     GMX_ASSERT(
 425             fr->pairsTable->interaction == GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
 426             "Pair interaction kernels need a table with Coulomb, repulsion and dispersion entries");
 427
 428     const real epsfac = fr->ic->epsfac;
 429
 430     bFreeEnergy = FALSE;
 431     for (i = 0; (i < nbonds);)
 432     {
 433         itype = iatoms[i++];
 434         ai    = iatoms[i++];
 435         aj    = iatoms[i++];
 436         gid   = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
 437
 438         /* Get parameters */
 439         switch (ftype)
 440         {
 441             case F_LJ14:
 442                 bFreeEnergy = (fr->efep != FreeEnergyPerturbationType::No
 443                                && (((md->nPerturbed != 0) && (md->bPerturbed[ai] || md->bPerturbed[aj]))
 444                                    || iparams[itype].lj14.c6A != iparams[itype].lj14.c6B
 445                                    || iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
 446                 qq          = md->chargeA[ai] * md->chargeA[aj] * epsfac * fr->fudgeQQ;
 447                 c6          = iparams[itype].lj14.c6A;
 448                 c12         = iparams[itype].lj14.c12A;
 449                 break;
 450             case F_LJC14_Q:
 451                 qq = iparams[itype].ljc14.qi * iparams[itype].ljc14.qj * epsfac
 452                      * iparams[itype].ljc14.fqq;
 453                 c6  = iparams[itype].ljc14.c6;
 454                 c12 = iparams[itype].ljc14.c12;
 455                 break;
 456             case F_LJC_PAIRS_NB:
 457                 qq  = iparams[itype].ljcnb.qi * iparams[itype].ljcnb.qj * epsfac;
 458                 c6  = iparams[itype].ljcnb.c6;
 459                 c12 = iparams[itype].ljcnb.c12;
 460                 break;
 461             default:
 462                 /* Cannot happen since we called gmx_fatal() above in this case */
 463                 qq = c6 = c12 = 0; /* Keep compiler happy */
 464                 break;
 465         }
 466
 467         /* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
 468          * included in the general nfbp array now. This means the tables are scaled down by the
 469          * same factor, so when we use the original c6/c12 parameters from iparams[] they must
 470          * be scaled up.
 471          */
 472         c6 *= 6.0;
 473         c12 *= 12.0;
 474
 475         /* Do we need to apply full periodic boundary conditions? */
 476         if (fr->bMolPBC)
 477         {
 478             fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
 479         }
 480         else
 481         {
 482             fshift_index = CENTRAL;
 483             rvec_sub(x[ai], x[aj], dx);
 484         }
 485         r2 = norm2(dx);
 486
 487         if (r2 >= fr->pairsTable->r * fr->pairsTable->r)
 488         {
 489             /* This check isn't race free. But it doesn't matter because if a race occurs the only
 490              * disadvantage is that the warning is printed twice */
 491             if (!warned_rlimit)
 492             {
 493                 warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->pairsTable->r);
 494                 warned_rlimit = TRUE;
 495             }
 496             continue;
 497         }
 498
 499         if (bFreeEnergy)
 500         {
 501             /* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
 502             qqB  = md->chargeB[ai] * md->chargeB[aj] * epsfac * fr->fudgeQQ;
 503             c6B  = iparams[itype].lj14.c6B * 6.0;
 504             c12B = iparams[itype].lj14.c12B * 12.0;
 505
 506             fscal = free_energy_evaluate_single(r2,
 507                                                 *fr->ic->softCoreParameters,
 508                                                 fr->pairsTable->scale,
 509                                                 fr->pairsTable->data.data(),
 510                                                 fr->pairsTable->stride,
 511                                                 qq,
 512                                                 c6,
 513                                                 c12,
 514                                                 qqB,
 515                                                 c6B,
 516                                                 c12B,
 517                                                 LFC,
 518                                                 LFV,
 519                                                 DLF,
 520                                                 lfac_coul,
 521                                                 lfac_vdw,
 522                                                 dlfac_coul,
 523                                                 dlfac_vdw,
 524                                                 &velec,
 525                                                 &vvdw,
 526                                                 dvdl);
 527         }
 528         else
 529         {
 530             /* Evaluate tabulated interaction without free energy */
 531             fscal = evaluate_single(r2,
 532                                     fr->pairsTable->scale,
 533                                     fr->pairsTable->data.data(),
 534                                     fr->pairsTable->stride,
 535                                     qq,
 536                                     c6,
 537                                     c12,
 538                                     &velec,
 539                                     &vvdw);
 540         }
 541
 542         energygrp_elec[gid] += velec;
 543         energygrp_vdw[gid] += vvdw;
 544         svmul(fscal, dx, dx);
 545
 546         /* Add the forces */
 547         rvec_inc(f[ai], dx);
 548         rvec_dec(f[aj], dx);
 549
 550         if (computeVirial(flavor))
 551         {
 552             if (fshift_index != CENTRAL)
 553             {
 554                 rvec_inc(fshift[fshift_index], dx);
 555                 rvec_dec(fshift[CENTRAL], dx);
 556             }
 557         }
 558     }
 559     return 0.0;
 560 }
 561
 562 /*! \brief Calculate pairs, only for plain-LJ + plain Coulomb normal type.
 563  *
 564  * This function is templated for real/SimdReal and for optimization.
 565  */
 566 template<typename T, int pack_size, typename pbc_type>
 567 static void do_pairs_simple(int              nbonds,
 568                             const t_iatom    iatoms[],
 569                             const t_iparams  iparams[],
 570                             const rvec       x[],
 571                             rvec4            f[],
 572                             const pbc_type   pbc,
 573                             const t_mdatoms* md,
 574                             const real       scale_factor)
 575 {
 576     const int nfa1 = 1 + 2;
 577
 578     T six(6);
 579     T twelve(12);
 580     T ef(scale_factor);
 581
 582 #if GMX_SIMD_HAVE_REAL
 583     alignas(GMX_SIMD_ALIGNMENT) std::int32_t ai[pack_size];
 584     alignas(GMX_SIMD_ALIGNMENT) std::int32_t aj[pack_size];
 585     alignas(GMX_SIMD_ALIGNMENT) real         coeff[3 * pack_size];
 586 #else
 587     std::int32_t ai[pack_size];
 588     std::int32_t aj[pack_size];
 589     real         coeff[3 * pack_size];
 590 #endif
 591
 592     /* nbonds is #pairs*nfa1, here we step pack_size pairs */
 593     for (int i = 0; i < nbonds; i += pack_size * nfa1)
 594     {
 595         /* Collect atoms for pack_size pairs.
 596          * iu indexes into iatoms, we should not let iu go beyond nbonds.
 597          */
 598         int iu = i;
 599         for (int s = 0; s < pack_size; s++)
 600         {
 601             int itype = iatoms[iu];
 602             ai[s]     = iatoms[iu + 1];
 603             aj[s]     = iatoms[iu + 2];
 604
 605             if (i + s * nfa1 < nbonds)
 606             {
 607                 coeff[0 * pack_size + s] = iparams[itype].lj14.c6A;
 608                 coeff[1 * pack_size + s] = iparams[itype].lj14.c12A;
 609                 coeff[2 * pack_size + s] = md->chargeA[ai[s]] * md->chargeA[aj[s]];
 610
 611                 /* Avoid indexing the iatoms array out of bounds.
 612                  * We pad the coordinate indices with the last atom pair.
 613                  */
 614                 if (iu + nfa1 < nbonds)
 615                 {
 616                     iu += nfa1;
 617                 }
 618             }
 619             else
 620             {
 621                 /* Pad the coefficient arrays with zeros to get zero forces */
 622                 coeff[0 * pack_size + s] = 0;
 623                 coeff[1 * pack_size + s] = 0;
 624                 coeff[2 * pack_size + s] = 0;
 625             }
 626         }
 627
 628         /* Load the coordinates */
 629         T xi[DIM], xj[DIM];
 630         gatherLoadUTranspose<3>(reinterpret_cast<const real*>(x), ai, &xi[XX], &xi[YY], &xi[ZZ]);
 631         gatherLoadUTranspose<3>(reinterpret_cast<const real*>(x), aj, &xj[XX], &xj[YY], &xj[ZZ]);
 632
 633         T c6  = load<T>(coeff + 0 * pack_size);
 634         T c12 = load<T>(coeff + 1 * pack_size);
 635         T qq  = load<T>(coeff + 2 * pack_size);
 636
 637         /* We could save these operations by storing 6*C6,12*C12 */
 638         c6  = six * c6;
 639         c12 = twelve * c12;
 640
 641         T dr[DIM];
 642         pbc_dx_aiuc(pbc, xi, xj, dr);
 643
 644         T rsq   = dr[XX] * dr[XX] + dr[YY] * dr[YY] + dr[ZZ] * dr[ZZ];
 645         T rinv  = gmx::invsqrt(rsq);
 646         T rinv2 = rinv * rinv;
 647         T rinv6 = rinv2 * rinv2 * rinv2;
 648
 649         /* Calculate the Coulomb force * r */
 650         T cfr = ef * qq * rinv;
 651
 652         /* Calculate the LJ force * r and add it to the Coulomb part */
 653         T fr = gmx::fma(fms(c12, rinv6, c6), rinv6, cfr);
 654
 655         T finvr = fr * rinv2;
 656         T fx    = finvr * dr[XX];
 657         T fy    = finvr * dr[YY];
 658         T fz    = finvr * dr[ZZ];
 659
 660         /* Add the pair forces to the force array.
 661          * Note that here we might add multiple force components for some atoms
 662          * due to the SIMD padding. But the extra force components are zero.
 663          */
 664         transposeScatterIncrU<4>(reinterpret_cast<real*>(f), ai, fx, fy, fz);
 665         transposeScatterDecrU<4>(reinterpret_cast<real*>(f), aj, fx, fy, fz);
 666     }
 667 }
 668
 669 /*! \brief Calculate all listed pair interactions */
 670 void do_pairs(int                      ftype,
 671               int                      nbonds,
 672               const t_iatom            iatoms[],
 673               const t_iparams          iparams[],
 674               const rvec               x[],
 675               rvec4                    f[],
 676               rvec                     fshift[],
 677               const struct t_pbc*      pbc,
 678               const real*              lambda,
 679               real*                    dvdl,
 680               const t_mdatoms*         md,
 681               const t_forcerec*        fr,
 682               const bool               havePerturbedInteractions,
 683               const gmx::StepWorkload& stepWork,
 684               gmx_grppairener_t*       grppener,
 685               int*                     global_atom_index)
 686 {
 687     if (ftype == F_LJ14 && fr->ic->vdwtype != VanDerWaalsType::User && !EEL_USER(fr->ic->eeltype)
 688         && !havePerturbedInteractions && (!stepWork.computeVirial && !stepWork.computeEnergy))
 689     {
 690         /* We use a fast code-path for plain LJ 1-4 without FEP.
 691          *
 692          * TODO: Add support for energies (straightforward) and virial
 693          * in the SIMD template. For the virial it's inconvenient to store
 694          * the force sums for the shifts and we should directly calculate
 695          * and sum the virial for the shifts. But we should do this
 696          * at once for the angles and dihedrals as well.
 697          */
 698 #if GMX_SIMD_HAVE_REAL
 699         if (fr->use_simd_kernels)
 700         {
 701             alignas(GMX_SIMD_ALIGNMENT) real pbc_simd[9 * GMX_SIMD_REAL_WIDTH];
 702             set_pbc_simd(pbc, pbc_simd);
 703
 704             do_pairs_simple<SimdReal, GMX_SIMD_REAL_WIDTH, const real*>(
 705                     nbonds, iatoms, iparams, x, f, pbc_simd, md, fr->ic->epsfac * fr->fudgeQQ);
 706         }
 707         else
 708 #endif
 709         {
 710             /* This construct is needed because pbc_dx_aiuc doesn't accept pbc=NULL */
 711             t_pbc        pbc_no;
 712             const t_pbc* pbc_nonnull;
 713
 714             if (pbc != nullptr)
 715             {
 716                 pbc_nonnull = pbc;
 717             }
 718             else
 719             {
 720                 set_pbc(&pbc_no, PbcType::No, nullptr);
 721                 pbc_nonnull = &pbc_no;
 722             }
 723
 724             do_pairs_simple<real, 1, const t_pbc*>(
 725                     nbonds, iatoms, iparams, x, f, pbc_nonnull, md, fr->ic->epsfac * fr->fudgeQQ);
 726         }
 727     }
 728     else if (stepWork.computeVirial)
 729     {
 730         do_pairs_general<BondedKernelFlavor::ForcesAndVirialAndEnergy>(
 731                 ftype, nbonds, iatoms, iparams, x, f, fshift, pbc, lambda, dvdl, md, fr, grppener, global_atom_index);
 732     }
 733     else
 734     {
 735         do_pairs_general<BondedKernelFlavor::ForcesAndEnergy>(
 736                 ftype, nbonds, iatoms, iparams, x, f, fshift, pbc, lambda, dvdl, md, fr, grppener, global_atom_index);
 737     }
 738 }