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37 * \brief This file defines functions for "pair" interactions
38 * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
40 * \author Mark Abraham <mark.j.abraham@gmail.com>
42 * \ingroup module_listed-forces
50 #include "gromacs/math/functions.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/mdtypes/group.h"
53 #include "gromacs/mdtypes/md_enums.h"
54 #include "gromacs/mdtypes/nblist.h"
55 #include "gromacs/pbcutil/ishift.h"
56 #include "gromacs/pbcutil/mshift.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/pbcutil/pbc-simd.h"
59 #include "gromacs/simd/simd.h"
60 #include "gromacs/simd/simd_math.h"
61 #include "gromacs/simd/vector_operations.h"
62 #include "gromacs/tables/forcetable.h"
63 #include "gromacs/utility/basedefinitions.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/gmxassert.h"
67 #include "listed-internal.h"
69 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
71 /*! \brief Issue a warning if a listed interaction is beyond a table limit */
73 warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
75 gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
76 "at distance %.3f which is larger than the table limit %.3f nm.\n\n"
77 "This is likely either a 1,4 interaction, or a listed interaction inside\n"
78 "a smaller molecule you are decoupling during a free energy calculation.\n"
79 "Since interactions at distances beyond the table cannot be computed,\n"
80 "they are skipped until they are inside the table limit again. You will\n"
81 "only see this message once, even if it occurs for several interactions.\n\n"
82 "IMPORTANT: This should not happen in a stable simulation, so there is\n"
83 "probably something wrong with your system. Only change the table-extension\n"
84 "distance in the mdp file if you are really sure that is the reason.\n",
85 glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
90 "%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
91 x[ai][XX], x[ai][YY], x[ai][ZZ], x[aj][XX], x[aj][YY], x[aj][ZZ],
92 glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r);
96 /*! \brief Compute the energy and force for a single pair interaction */
98 evaluate_single(real r2, real tabscale, real *vftab, real tableStride,
99 real qq, real c6, real c12, real *velec, real *vvdw)
101 real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
104 /* Do the tabulated interactions - first table lookup */
105 rinv = gmx::invsqrt(r2);
108 ntab = static_cast<int>(rtab);
111 ntab = tableStride*ntab;
115 Geps = eps*vftab[ntab+2];
116 Heps2 = eps2*vftab[ntab+3];
119 FFe = Fp+Geps+2.0*Heps2;
123 Geps = eps*vftab[ntab+6];
124 Heps2 = eps2*vftab[ntab+7];
127 FFd = Fp+Geps+2.0*Heps2;
131 Geps = eps*vftab[ntab+10];
132 Heps2 = eps2*vftab[ntab+11];
135 FFr = Fp+Geps+2.0*Heps2;
138 *vvdw = c6*VVd+c12*VVr;
140 fscal = -(qq*FFe+c6*FFd+c12*FFr)*tabscale*rinv;
145 /*! \brief Compute the energy and force for a single pair interaction under FEP */
147 free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul,
148 real alpha_vdw, real tabscale, real *vftab, real tableStride,
149 real qqA, real c6A, real c12A, real qqB,
150 real c6B, real c12B, real LFC[2], real LFV[2], real DLF[2],
151 real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2],
152 real dlfac_vdw[2], real sigma6_def, real sigma6_min,
153 real sigma2_def, real sigma2_min,
154 real *velectot, real *vvdwtot, real *dvdl)
156 real rp, rpm2, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
157 real qq[2], c6[2], c12[2], sigma6[2], sigma2[2], sigma_pow[2];
158 real alpha_coul_eff, alpha_vdw_eff, dvdl_coul, dvdl_vdw;
159 real rpinv, r_coul, r_vdw, velecsum, vvdwsum;
160 real fscal_vdw[2], fscal_elec[2];
161 real velec[2], vvdw[2];
163 const real half = 0.5;
164 const real minusOne = -1.0;
165 const real one = 1.0;
166 const real two = 2.0;
167 const real six = 6.0;
168 const real fourtyeight = 48.0;
177 if (sc_r_power == six)
179 rpm2 = r2*r2; /* r4 */
180 rp = rpm2*r2; /* r6 */
182 else if (sc_r_power == fourtyeight)
184 rp = r2*r2*r2; /* r6 */
185 rp = rp*rp; /* r12 */
186 rp = rp*rp; /* r24 */
187 rp = rp*rp; /* r48 */
188 rpm2 = rp/r2; /* r46 */
192 rp = std::pow(r2, half * sc_r_power); /* not currently supported as input, but can handle it */
196 /* Loop over state A(0) and B(1) */
197 for (i = 0; i < 2; i++)
199 if ((c6[i] > 0) && (c12[i] > 0))
201 /* The c6 & c12 coefficients now contain the constants 6.0 and 12.0, respectively.
202 * Correct for this by multiplying with (1/12.0)/(1/6.0)=6.0/12.0=0.5.
204 sigma6[i] = half*c12[i]/c6[i];
205 sigma2[i] = std::cbrt(half*c12[i]/c6[i]);
206 /* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
207 what data to store externally. Can't be fixed without larger scale changes, so not 5.0 */
208 if (sigma6[i] < sigma6_min) /* for disappearing coul and vdw with soft core at the same time */
210 sigma6[i] = sigma6_min;
211 sigma2[i] = sigma2_min;
216 sigma6[i] = sigma6_def;
217 sigma2[i] = sigma2_def;
219 if (sc_r_power == six)
221 sigma_pow[i] = sigma6[i];
223 else if (sc_r_power == fourtyeight)
225 sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
226 sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
227 sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^48 */
230 { /* not really supported as input, but in here for testing the general case*/
231 sigma_pow[i] = std::pow(sigma2[i], sc_r_power/2);
235 /* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
236 if ((c12[0] > 0) && (c12[1] > 0))
243 alpha_vdw_eff = alpha_vdw;
244 alpha_coul_eff = alpha_coul;
247 /* Loop over A and B states again */
248 for (i = 0; i < 2; i++)
255 /* Only spend time on A or B state if it is non-zero */
256 if ( (qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0) )
259 rpinv = one/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
260 r_coul = std::pow(rpinv, minusOne / sc_r_power);
262 /* Electrostatics table lookup data */
263 rtab = r_coul*tabscale;
264 ntab = static_cast<int>(rtab);
267 ntab = tableStride*ntab;
271 Geps = eps*vftab[ntab+2];
272 Heps2 = eps2*vftab[ntab+3];
275 FF = Fp+Geps+two*Heps2;
277 fscal_elec[i] = -qq[i]*FF*r_coul*rpinv*tabscale;
280 rpinv = one/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
281 r_vdw = std::pow(rpinv, minusOne / sc_r_power);
282 /* Vdw table lookup data */
283 rtab = r_vdw*tabscale;
284 ntab = static_cast<int>(rtab);
291 Geps = eps*vftab[ntab+6];
292 Heps2 = eps2*vftab[ntab+7];
295 FF = Fp+Geps+two*Heps2;
297 fscal_vdw[i] = -c6[i]*FF;
302 Geps = eps*vftab[ntab+10];
303 Heps2 = eps2*vftab[ntab+11];
306 FF = Fp+Geps+two*Heps2;
307 vvdw[i] += c12[i]*VV;
308 fscal_vdw[i] -= c12[i]*FF;
309 fscal_vdw[i] *= r_vdw*rpinv*tabscale;
312 /* Now we have velec[i], vvdw[i], and fscal[i] for both states */
313 /* Assemble A and B states */
319 for (i = 0; i < 2; i++)
321 velecsum += LFC[i]*velec[i];
322 vvdwsum += LFV[i]*vvdw[i];
324 fscal += (LFC[i]*fscal_elec[i]+LFV[i]*fscal_vdw[i])*rpm2;
326 dvdl_coul += velec[i]*DLF[i] + LFC[i]*alpha_coul_eff*dlfac_coul[i]*fscal_elec[i]*sigma_pow[i];
327 dvdl_vdw += vvdw[i]*DLF[i] + LFV[i]*alpha_vdw_eff*dlfac_vdw[i]*fscal_vdw[i]*sigma_pow[i];
330 dvdl[efptCOUL] += dvdl_coul;
331 dvdl[efptVDW] += dvdl_vdw;
333 *velectot = velecsum;
339 /*! \brief Calculate pair interactions, supports all types and conditions. */
341 do_pairs_general(int ftype, int nbonds,
342 const t_iatom iatoms[], const t_iparams iparams[],
343 const rvec x[], rvec4 f[], rvec fshift[],
344 const struct t_pbc *pbc, const struct t_graph *g,
345 real *lambda, real *dvdl,
347 const t_forcerec *fr, gmx_grppairener_t *grppener,
348 int *global_atom_index)
353 int i, itype, ai, aj, gid;
356 real fscal, velec, vvdw;
357 real * energygrp_elec;
358 real * energygrp_vdw;
359 static gmx_bool warned_rlimit = FALSE;
360 /* Free energy stuff */
361 gmx_bool bFreeEnergy;
362 real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
363 real qqB, c6B, c12B, sigma2_def, sigma2_min;
369 energygrp_elec = grppener->ener[egCOUL14];
370 energygrp_vdw = grppener->ener[egLJ14];
373 energygrp_elec = grppener->ener[egCOULSR];
374 energygrp_vdw = grppener->ener[egLJSR];
377 energygrp_elec = nullptr; /* Keep compiler happy */
378 energygrp_vdw = nullptr; /* Keep compiler happy */
379 gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
383 if (fr->efep != efepNO)
385 /* Lambda factor for state A=1-lambda and B=lambda */
386 LFC[0] = 1.0 - lambda[efptCOUL];
387 LFV[0] = 1.0 - lambda[efptVDW];
388 LFC[1] = lambda[efptCOUL];
389 LFV[1] = lambda[efptVDW];
391 /*derivative of the lambda factor for state A and B */
396 sigma2_def = std::cbrt(fr->sc_sigma6_def);
397 sigma2_min = std::cbrt(fr->sc_sigma6_min);
399 for (i = 0; i < 2; i++)
401 lfac_coul[i] = (fr->sc_power == 2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
402 dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFC[i]) : 1);
403 lfac_vdw[i] = (fr->sc_power == 2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
404 dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFV[i]) : 1);
409 sigma2_min = sigma2_def = 0;
412 /* TODO This code depends on the logic in tables.c that constructs
413 the table layout, which should be made explicit in future
415 GMX_ASSERT(etiNR == 3, "Pair-interaction code that uses GROMACS interaction tables supports exactly 3 tables");
416 GMX_ASSERT(fr->pairsTable->interaction == GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
417 "Pair interaction kernels need a table with Coulomb, repulsion and dispersion entries");
420 for (i = 0; (i < nbonds); )
425 gid = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
432 (fr->efep != efepNO &&
433 ((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
434 iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
435 iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
436 qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
437 c6 = iparams[itype].lj14.c6A;
438 c12 = iparams[itype].lj14.c12A;
441 qq = iparams[itype].ljc14.qi*iparams[itype].ljc14.qj*fr->epsfac*iparams[itype].ljc14.fqq;
442 c6 = iparams[itype].ljc14.c6;
443 c12 = iparams[itype].ljc14.c12;
446 qq = iparams[itype].ljcnb.qi*iparams[itype].ljcnb.qj*fr->epsfac;
447 c6 = iparams[itype].ljcnb.c6;
448 c12 = iparams[itype].ljcnb.c12;
451 /* Cannot happen since we called gmx_fatal() above in this case */
452 qq = c6 = c12 = 0; /* Keep compiler happy */
456 /* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
457 * included in the general nfbp array now. This means the tables are scaled down by the
458 * same factor, so when we use the original c6/c12 parameters from iparams[] they must
464 /* Do we need to apply full periodic boundary conditions? */
465 if (fr->bMolPBC == TRUE)
467 fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
471 fshift_index = CENTRAL;
472 rvec_sub(x[ai], x[aj], dx);
476 if (r2 >= fr->pairsTable->r*fr->pairsTable->r)
478 /* This check isn't race free. But it doesn't matter because if a race occurs the only
479 * disadvantage is that the warning is printed twice */
480 if (warned_rlimit == FALSE)
482 warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->pairsTable->r);
483 warned_rlimit = TRUE;
490 /* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
491 qqB = md->chargeB[ai]*md->chargeB[aj]*fr->epsfac*fr->fudgeQQ;
492 c6B = iparams[itype].lj14.c6B*6.0;
493 c12B = iparams[itype].lj14.c12B*12.0;
495 fscal = free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
496 fr->pairsTable->scale, fr->pairsTable->data, fr->pairsTable->stride,
497 qq, c6, c12, qqB, c6B, c12B,
498 LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
499 fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
503 /* Evaluate tabulated interaction without free energy */
504 fscal = evaluate_single(r2, fr->pairsTable->scale, fr->pairsTable->data, fr->pairsTable->stride,
505 qq, c6, c12, &velec, &vvdw);
508 energygrp_elec[gid] += velec;
509 energygrp_vdw[gid] += vvdw;
510 svmul(fscal, dx, dx);
518 /* Correct the shift forces using the graph */
519 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
520 fshift_index = IVEC2IS(dt);
522 if (fshift_index != CENTRAL)
524 rvec_inc(fshift[fshift_index], dx);
525 rvec_dec(fshift[CENTRAL], dx);
531 /*! \brief Calculate pairs, only for plain-LJ + plain Coulomb normal type.
533 * This function is templated for real/SimdReal and for optimization.
535 template<typename T, int pack_size,
538 do_pairs_simple(int nbonds,
539 const t_iatom iatoms[], const t_iparams iparams[],
540 const rvec x[], rvec4 f[],
543 const real scale_factor)
545 const int nfa1 = 1 + 2;
551 const int align = 16;
552 GMX_ASSERT(pack_size <= align, "align should be increased");
553 GMX_ALIGNED(int, align) ai[pack_size];
554 GMX_ALIGNED(int, align) aj[pack_size];
555 GMX_ALIGNED(real, align) coeff[3*pack_size];
557 /* nbonds is #pairs*nfa1, here we step pack_size pairs */
558 for (int i = 0; i < nbonds; i += pack_size*nfa1)
560 /* Collect atoms for pack_size pairs.
561 * iu indexes into iatoms, we should not let iu go beyond nbonds.
564 for (int s = 0; s < pack_size; s++)
566 int itype = iatoms[iu];
567 ai[s] = iatoms[iu + 1];
568 aj[s] = iatoms[iu + 2];
570 if (i + s*nfa1 < nbonds)
572 coeff[0*pack_size + s] = iparams[itype].lj14.c6A;
573 coeff[1*pack_size + s] = iparams[itype].lj14.c12A;
574 coeff[2*pack_size + s] = md->chargeA[ai[s]]*md->chargeA[aj[s]];
576 /* Avoid indexing the iatoms array out of bounds.
577 * We pad the coordinate indices with the last atom pair.
579 if (iu + nfa1 < nbonds)
586 /* Pad the coefficient arrays with zeros to get zero forces */
587 coeff[0*pack_size + s] = 0;
588 coeff[1*pack_size + s] = 0;
589 coeff[2*pack_size + s] = 0;
593 /* Load the coordinates */
595 gatherLoadUTranspose<3>(reinterpret_cast<const real *>(x), ai, &xi[XX], &xi[YY], &xi[ZZ]);
596 gatherLoadUTranspose<3>(reinterpret_cast<const real *>(x), aj, &xj[XX], &xj[YY], &xj[ZZ]);
598 T c6 = load(coeff + 0*pack_size);
599 T c12 = load(coeff + 1*pack_size);
600 T qq = load(coeff + 2*pack_size);
602 /* We could save these operations by storing 6*C6,12*C12 */
607 pbc_dx_aiuc(pbc, xi, xj, dr);
609 T rsq = dr[XX]*dr[XX] + dr[YY]*dr[YY] + dr[ZZ]*dr[ZZ];
610 T rinv = invsqrt(rsq);
612 T rinv6 = rinv2*rinv2*rinv2;
614 /* Calculate the Coulomb force * r */
617 /* Calculate the LJ force * r and add it to the Coulomb part */
618 T fr = gmx::fma(fms(c12, rinv6, c6), rinv6, cfr);
625 /* Add the pair forces to the force array.
626 * Note that here we might add multiple force components for some atoms
627 * due to the SIMD padding. But the extra force components are zero.
629 transposeScatterIncrU<4>(reinterpret_cast<real *>(f), ai, fx, fy, fz);
630 transposeScatterDecrU<4>(reinterpret_cast<real *>(f), aj, fx, fy, fz);
634 /*! \brief Calculate all listed pair interactions */
636 do_pairs(int ftype, int nbonds,
637 const t_iatom iatoms[], const t_iparams iparams[],
638 const rvec x[], rvec4 f[], rvec fshift[],
639 const struct t_pbc *pbc, const struct t_graph *g,
640 real *lambda, real *dvdl,
642 const t_forcerec *fr,
643 gmx_bool bCalcEnergyAndVirial, gmx_grppairener_t *grppener,
644 int *global_atom_index)
646 if (ftype == F_LJ14 &&
647 fr->vdwtype != evdwUSER && !EEL_USER(fr->eeltype) &&
648 !bCalcEnergyAndVirial && fr->efep == efepNO)
650 /* We use a fast code-path for plain LJ 1-4 without FEP.
652 * TODO: Add support for energies (straightforward) and virial
653 * in the SIMD template. For the virial it's inconvenient to store
654 * the force sums for the shifts and we should directly calculate
655 * and sum the virial for the shifts. But we should do this
656 * at once for the angles and dihedrals as well.
659 GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) pbc_simd[9*GMX_SIMD_REAL_WIDTH];
660 set_pbc_simd(pbc, pbc_simd);
662 do_pairs_simple<SimdReal, GMX_SIMD_REAL_WIDTH,
663 const real *>(nbonds, iatoms, iparams,
665 md, fr->epsfac*fr->fudgeQQ);
667 /* This construct is needed because pbc_dx_aiuc doesn't accept pbc=NULL */
669 const t_pbc *pbc_nonnull;
677 set_pbc(&pbc_no, epbcNONE, nullptr);
678 pbc_nonnull = &pbc_no;
681 do_pairs_simple<real, 1,
682 const t_pbc *>(nbonds, iatoms, iparams,
684 md, fr->epsfac*fr->fudgeQQ);
689 do_pairs_general(ftype, nbonds, iatoms, iparams,
690 x, f, fshift, pbc, g,
692 md, fr, grppener, global_atom_index);