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37 #include "dispersioncorrection.h"
41 #include "gromacs/math/units.h"
42 #include "gromacs/math/utilities.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/mdtypes/forcerec.h"
45 #include "gromacs/mdtypes/inputrec.h"
46 #include "gromacs/mdtypes/interaction_const.h"
47 #include "gromacs/mdtypes/md_enums.h"
48 #include "gromacs/tables/forcetable.h"
49 #include "gromacs/topology/mtop_util.h"
50 #include "gromacs/topology/topology.h"
51 #include "gromacs/utility/arrayref.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/logger.h"
55 /* Implementation here to avoid other files needing to include the file that defines t_nblists */
56 DispersionCorrection::InteractionParams::~InteractionParams() = default;
58 /* Returns a matrix, as flat list, of combination rule combined LJ parameters */
59 static std::vector<real> mk_nbfp_combination_rule(const gmx_ffparams_t& ffparams,
60 const CombinationRule comb_rule)
62 const int atnr = ffparams.atnr;
64 std::vector<real> nbfp(atnr * atnr * 2);
66 for (int i = 0; i < atnr; ++i)
68 for (int j = 0; j < atnr; ++j)
70 const real c6i = ffparams.iparams[i * (atnr + 1)].lj.c6;
71 const real c12i = ffparams.iparams[i * (atnr + 1)].lj.c12;
72 const real c6j = ffparams.iparams[j * (atnr + 1)].lj.c6;
73 const real c12j = ffparams.iparams[j * (atnr + 1)].lj.c12;
74 real c6 = std::sqrt(c6i * c6j);
75 real c12 = std::sqrt(c12i * c12j);
76 if (comb_rule == CombinationRule::Arithmetic && !gmx_numzero(c6) && !gmx_numzero(c12))
78 const real sigmai = gmx::sixthroot(c12i / c6i);
79 const real sigmaj = gmx::sixthroot(c12j / c6j);
80 const real epsi = c6i * c6i / c12i;
81 const real epsj = c6j * c6j / c12j;
82 const real sigma = 0.5 * (sigmai + sigmaj);
83 const real eps = std::sqrt(epsi * epsj);
84 c6 = eps * gmx::power6(sigma);
85 c12 = eps * gmx::power12(sigma);
87 C6(nbfp, atnr, i, j) = c6 * 6.0;
88 C12(nbfp, atnr, i, j) = c12 * 12.0;
95 /* Returns the A-topology atom type when aOrB=0, the B-topology atom type when aOrB=1 */
96 static int atomtypeAOrB(const t_atom& atom, int aOrB)
108 DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
109 const t_inputrec& inputrec,
112 gmx::ArrayRef<const real> nonbondedForceParameters)
114 const int ntp = numAtomTypes;
115 const gmx_bool bBHAM = useBuckingham;
117 gmx::ArrayRef<const real> nbfp = nonbondedForceParameters;
118 std::vector<real> nbfp_comb;
119 /* For LJ-PME, we want to correct for the difference between the
120 * actual C6 values and the C6 values used by the LJ-PME based on
121 * combination rules. */
122 if (EVDW_PME(inputrec.vdwtype))
124 nbfp_comb = mk_nbfp_combination_rule(mtop.ffparams,
125 (inputrec.ljpme_combination_rule == LongRangeVdW::LB)
126 ? CombinationRule::Arithmetic
127 : CombinationRule::Geometric);
128 for (int tpi = 0; tpi < ntp; ++tpi)
130 for (int tpj = 0; tpj < ntp; ++tpj)
132 C6(nbfp_comb, ntp, tpi, tpj) = C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
133 C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
139 for (int q = 0; q < (inputrec.efep == FreeEnergyPerturbationType::No ? 1 : 2); q++)
145 if (!EI_TPI(inputrec.eI))
147 numAtomsForDensity_ = mtop.natoms;
148 numCorrections_ = 0.5 * mtop.natoms;
150 /* Count the types so we avoid natoms^2 operations */
151 std::vector<int> typecount(ntp);
152 gmx_mtop_count_atomtypes(mtop, q, typecount.data());
154 for (int tpi = 0; tpi < ntp; tpi++)
156 for (int tpj = tpi; tpj < ntp; tpj++)
158 const int64_t iCount = typecount[tpi];
159 const int64_t jCount = typecount[tpj];
163 npair_ij = iCount * jCount;
167 npair_ij = iCount * (iCount - 1) / 2;
171 /* nbfp now includes the 6.0 derivative prefactor */
172 csix += npair_ij * BHAMC(nbfp, ntp, tpi, tpj) / 6.0;
176 /* nbfp now includes the 6.0/12.0 derivative prefactors */
177 csix += npair_ij * C6(nbfp, ntp, tpi, tpj) / 6.0;
178 ctwelve += npair_ij * C12(nbfp, ntp, tpi, tpj) / 12.0;
183 /* Subtract the excluded pairs.
184 * The main reason for substracting exclusions is that in some cases
185 * some combinations might never occur and the parameters could have
186 * any value. These unused values should not influence the dispersion
189 for (const gmx_molblock_t& molb : mtop.molblock)
191 const int nmol = molb.nmol;
192 const t_atoms* atoms = &mtop.moltype[molb.type].atoms;
193 const auto& excl = mtop.moltype[molb.type].excls;
194 for (int i = 0; (i < atoms->nr); i++)
196 const int tpi = atomtypeAOrB(atoms->atom[i], q);
197 for (const int k : excl[i])
201 const int tpj = atomtypeAOrB(atoms->atom[k], q);
204 /* nbfp now includes the 6.0 derivative prefactor */
205 csix -= nmol * BHAMC(nbfp, ntp, tpi, tpj) / 6.0;
209 /* nbfp now includes the 6.0/12.0 derivative prefactors */
210 csix -= nmol * C6(nbfp, ntp, tpi, tpj) / 6.0;
211 ctwelve -= nmol * C12(nbfp, ntp, tpi, tpj) / 12.0;
221 const t_atoms& atoms_tpi = mtop.moltype[mtop.molblock.back().type].atoms;
223 /* Only correct for the interaction of the test particle
224 * with the rest of the system.
226 numAtomsForDensity_ = mtop.natoms - atoms_tpi.nr;
227 numCorrections_ = atoms_tpi.nr;
230 for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
232 const gmx_molblock_t& molb = mtop.molblock[mb];
233 const t_atoms& atoms = mtop.moltype[molb.type].atoms;
234 for (int j = 0; j < atoms.nr; j++)
236 int nmolc = molb.nmol;
237 /* Remove the interaction of the test charge group
240 if (mb == mtop.molblock.size() - 1)
244 if (mb == 0 && molb.nmol == 1)
247 "Old format tpr with TPI, please generate a new tpr file");
250 const int tpj = atomtypeAOrB(atoms.atom[j], q);
251 for (int i = 0; i < atoms_tpi.nr; i++)
253 const int tpi = atomtypeAOrB(atoms_tpi.atom[i], q);
256 /* nbfp now includes the 6.0 derivative prefactor */
257 csix += nmolc * BHAMC(nbfp, ntp, tpi, tpj) / 6.0;
261 /* nbfp now includes the 6.0/12.0 derivative prefactors */
262 csix += nmolc * C6(nbfp, ntp, tpi, tpj) / 6.0;
263 ctwelve += nmolc * C12(nbfp, ntp, tpi, tpj) / 12.0;
270 if (npair - nexcl <= 0)
277 csix /= npair - nexcl;
278 ctwelve /= npair - nexcl;
282 fprintf(debug, "Counted %" PRId64 " exclusions\n", nexcl);
283 fprintf(debug, "Average C6 parameter is: %10g\n", csix);
284 fprintf(debug, "Average C12 parameter is: %10g\n", ctwelve);
287 avctwelve_[q] = ctwelve;
291 static void integrate_table(const real vdwtab[],
299 const double invscale = 1.0 / scale;
300 const double invscale2 = invscale * invscale;
301 const double invscale3 = invscale * invscale2;
303 /* Following summation derived from cubic spline definition,
304 * Numerical Recipies in C, second edition, p. 113-116. Exact for
305 * the cubic spline. We first calculate the negative of the
306 * energy from rvdw to rvdw_switch, assuming that g(r)=1, and then
307 * add the more standard, abrupt cutoff correction to that result,
308 * yielding the long-range correction for a switched function. We
309 * perform both the pressure and energy loops at the same time for
310 * simplicity, as the computational cost is low. */
312 /* Since the dispersion table has been scaled down a factor
313 * 6.0 and the repulsion a factor 12.0 to compensate for the
314 * c6/c12 parameters inside nbfp[] being scaled up (to save
315 * flops in kernels), we need to correct for this.
317 const double tabfactor = (offstart == 0 ? 6.0 : 12.0);
319 double enersum = 0.0;
321 for (int ri = rstart; ri < rend; ++ri)
323 const double r = ri * invscale;
324 const double ea = invscale3;
325 const double eb = 2.0 * invscale2 * r;
326 const double ec = invscale * r * r;
328 const double pa = invscale3;
329 const double pb = 3.0 * invscale2 * r;
330 const double pc = 3.0 * invscale * r * r;
331 const double pd = r * r * r;
333 /* this "8" is from the packing in the vdwtab array - perhaps
334 should be defined? */
336 const int offset = 8 * ri + offstart;
337 const double y0 = vdwtab[offset];
338 const double f = vdwtab[offset + 1];
339 const double g = vdwtab[offset + 2];
340 const double h = vdwtab[offset + 3];
342 enersum += y0 * (ea / 3 + eb / 2 + ec) + f * (ea / 4 + eb / 3 + ec / 2)
343 + g * (ea / 5 + eb / 4 + ec / 3) + h * (ea / 6 + eb / 5 + ec / 4);
344 virsum += f * (pa / 4 + pb / 3 + pc / 2 + pd) + 2 * g * (pa / 5 + pb / 4 + pc / 3 + pd / 2)
345 + 3 * h * (pa / 6 + pb / 5 + pc / 4 + pd / 3);
347 *enerout = 4.0 * M_PI * enersum * tabfactor;
348 *virout = 4.0 * M_PI * virsum * tabfactor;
351 /* Struct for storing and passing energy or virial corrections */
352 struct InteractionCorrection
358 /* Adds the energy and virial corrections beyond the cut-off */
359 static void addCorrectionBeyondCutoff(InteractionCorrection* energy,
360 InteractionCorrection* virial,
361 const double cutoffDistance)
363 const double rc3 = cutoffDistance * cutoffDistance * cutoffDistance;
364 const double rc9 = rc3 * rc3 * rc3;
366 energy->dispersion += -4.0 * M_PI / (3.0 * rc3);
367 energy->repulsion += 4.0 * M_PI / (9.0 * rc9);
368 virial->dispersion += 8.0 * M_PI / rc3;
369 virial->repulsion += -16.0 * M_PI / (3.0 * rc9);
372 void DispersionCorrection::setInteractionParameters(InteractionParams* iParams,
373 const interaction_const_t& ic,
374 const char* tableFileName)
376 /* We only need to set the tables at first call, i.e. tableFileName!=nullptr
377 * or when we changed the cut-off with LJ-PME tuning.
379 if (tableFileName || EVDW_PME(ic.vdwtype))
381 iParams->dispersionCorrectionTable_ =
382 makeDispersionCorrectionTable(nullptr, &ic, ic.rvdw, tableFileName);
385 InteractionCorrection energy;
386 InteractionCorrection virial;
388 if ((ic.vdw_modifier == InteractionModifiers::PotShift)
389 || (ic.vdw_modifier == InteractionModifiers::PotSwitch)
390 || (ic.vdw_modifier == InteractionModifiers::ForceSwitch)
391 || (ic.vdwtype == VanDerWaalsType::Shift) || (ic.vdwtype == VanDerWaalsType::Switch))
393 if (((ic.vdw_modifier == InteractionModifiers::PotSwitch)
394 || (ic.vdw_modifier == InteractionModifiers::ForceSwitch)
395 || (ic.vdwtype == VanDerWaalsType::Switch))
396 && ic.rvdw_switch == 0)
399 "With dispersion correction rvdw-switch can not be zero "
401 enumValueToString(ic.vdwtype));
404 GMX_ASSERT(iParams->dispersionCorrectionTable_, "We need an initialized table");
406 /* TODO This code depends on the logic in tables.c that
407 constructs the table layout, which should be made
408 explicit in future cleanup. */
409 GMX_ASSERT(iParams->dispersionCorrectionTable_->interaction == TableInteraction::VdwRepulsionVdwDispersion,
410 "Dispersion-correction code needs a table with both repulsion and dispersion "
412 const real scale = iParams->dispersionCorrectionTable_->scale;
413 const real* vdwtab = iParams->dispersionCorrectionTable_->data.data();
415 /* Round the cut-offs to exact table values for precision */
416 int ri0 = static_cast<int>(std::floor(ic.rvdw_switch * scale));
417 int ri1 = static_cast<int>(std::ceil(ic.rvdw * scale));
419 /* The code below has some support for handling force-switching, i.e.
420 * when the force (instead of potential) is switched over a limited
421 * region. This leads to a constant shift in the potential inside the
422 * switching region, which we can handle by adding a constant energy
423 * term in the force-switch case just like when we do potential-shift.
425 * For now this is not enabled, but to keep the functionality in the
426 * code we check separately for switch and shift. When we do force-switch
427 * the shifting point is rvdw_switch, while it is the cutoff when we
428 * have a classical potential-shift.
430 * For a pure potential-shift the potential has a constant shift
431 * all the way out to the cutoff, and that is it. For other forms
432 * we need to calculate the constant shift up to the point where we
433 * start modifying the potential.
435 ri0 = (ic.vdw_modifier == InteractionModifiers::PotShift) ? ri1 : ri0;
437 const double r0 = ri0 / scale;
438 const double rc3 = r0 * r0 * r0;
439 const double rc9 = rc3 * rc3 * rc3;
441 if ((ic.vdw_modifier == InteractionModifiers::ForceSwitch) || (ic.vdwtype == VanDerWaalsType::Shift))
443 /* Determine the constant energy shift below rvdw_switch.
444 * Table has a scale factor since we have scaled it down to compensate
445 * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
447 iParams->enershiftsix_ = static_cast<real>(-1.0 / (rc3 * rc3)) - 6.0 * vdwtab[8 * ri0];
448 iParams->enershifttwelve_ = static_cast<real>(1.0 / (rc9 * rc3)) - 12.0 * vdwtab[8 * ri0 + 4];
450 else if (ic.vdw_modifier == InteractionModifiers::PotShift)
452 iParams->enershiftsix_ = static_cast<real>(-1.0 / (rc3 * rc3));
453 iParams->enershifttwelve_ = static_cast<real>(1.0 / (rc9 * rc3));
456 /* Add the constant part from 0 to rvdw_switch.
457 * This integration from 0 to rvdw_switch overcounts the number
458 * of interactions by 1, as it also counts the self interaction.
459 * We will correct for this later.
461 energy.dispersion += 4.0 * M_PI * iParams->enershiftsix_ * rc3 / 3.0;
462 energy.repulsion += 4.0 * M_PI * iParams->enershifttwelve_ * rc3 / 3.0;
464 /* Calculate the contribution in the range [r0,r1] where we
465 * modify the potential. For a pure potential-shift modifier we will
466 * have ri0==ri1, and there will not be any contribution here.
470 integrate_table(vdwtab, scale, 0, ri0, ri1, &enersum, &virsum);
471 energy.dispersion -= enersum;
472 virial.dispersion -= virsum;
473 integrate_table(vdwtab, scale, 4, ri0, ri1, &enersum, &virsum);
474 energy.repulsion -= enersum;
475 virial.repulsion -= virsum;
478 /* Alright: Above we compensated by REMOVING the parts outside r0
479 * corresponding to the ideal VdW 1/r6 and /r12 potentials.
481 * Regardless of whether r0 is the point where we start switching,
482 * or the cutoff where we calculated the constant shift, we include
483 * all the parts we are missing out to infinity from r0 by
484 * calculating the analytical dispersion correction.
486 addCorrectionBeyondCutoff(&energy, &virial, r0);
488 else if (ic.vdwtype == VanDerWaalsType::Cut || EVDW_PME(ic.vdwtype)
489 || ic.vdwtype == VanDerWaalsType::User)
491 /* Note that with LJ-PME, the dispersion correction is multiplied
492 * by the difference between the actual C6 and the value of C6
493 * that would produce the combination rule.
494 * This means the normal energy and virial difference formulas
498 const double rc3 = ic.rvdw * ic.rvdw * ic.rvdw;
499 const double rc9 = rc3 * rc3 * rc3;
500 if (ic.vdw_modifier == InteractionModifiers::PotShift)
502 /* Contribution within the cut-off */
503 energy.dispersion += -4.0 * M_PI / (3.0 * rc3);
504 energy.repulsion += 4.0 * M_PI / (3.0 * rc9);
506 /* Contribution beyond the cut-off */
507 addCorrectionBeyondCutoff(&energy, &virial, ic.rvdw);
512 "Dispersion correction is not implemented for vdw-type = %s",
513 enumValueToString(ic.vdwtype));
516 iParams->enerdiffsix_ = energy.dispersion;
517 iParams->enerdifftwelve_ = energy.repulsion;
518 /* The 0.5 is due to the Gromacs definition of the virial */
519 iParams->virdiffsix_ = 0.5 * virial.dispersion;
520 iParams->virdifftwelve_ = 0.5 * virial.repulsion;
523 DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
524 const t_inputrec& inputrec,
527 gmx::ArrayRef<const real> nonbondedForceParameters,
528 const interaction_const_t& ic,
529 const char* tableFileName) :
530 eDispCorr_(inputrec.eDispCorr),
531 vdwType_(inputrec.vdwtype),
532 eFep_(inputrec.efep),
533 topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
535 if (eDispCorr_ != DispersionCorrectionType::No)
537 GMX_RELEASE_ASSERT(tableFileName, "Need a table file name");
539 setInteractionParameters(&iParams_, ic, tableFileName);
543 bool DispersionCorrection::correctFullInteraction() const
545 return (eDispCorr_ == DispersionCorrectionType::AllEner
546 || eDispCorr_ == DispersionCorrectionType::AllEnerPres);
549 void DispersionCorrection::print(const gmx::MDLogger& mdlog) const
551 if (topParams_.avcsix_[0] == 0 && topParams_.avctwelve_[0] == 0)
553 GMX_LOG(mdlog.warning)
555 .appendText("WARNING: There are no atom pairs for dispersion correction");
557 else if (vdwType_ == VanDerWaalsType::User)
559 GMX_LOG(mdlog.warning)
561 .appendText("WARNING: using dispersion correction with user tables\n");
564 std::string text = gmx::formatString("Long Range LJ corr.: <C6> %10.4e", topParams_.avcsix_[0]);
565 if (correctFullInteraction())
567 text += gmx::formatString(" <C12> %10.4e", topParams_.avctwelve_[0]);
569 GMX_LOG(mdlog.info).appendText(text);
572 void DispersionCorrection::setParameters(const interaction_const_t& ic)
574 if (eDispCorr_ != DispersionCorrectionType::No)
576 setInteractionParameters(&iParams_, ic, nullptr);
580 DispersionCorrection::Correction DispersionCorrection::calculate(const matrix box, const real lambda) const
585 if (eDispCorr_ == DispersionCorrectionType::No)
590 const bool bCorrAll = correctFullInteraction();
591 const bool bCorrPres = (eDispCorr_ == DispersionCorrectionType::EnerPres
592 || eDispCorr_ == DispersionCorrectionType::AllEnerPres);
594 const real invvol = 1 / det(box);
595 const real density = topParams_.numAtomsForDensity_ * invvol;
596 const real numCorr = topParams_.numCorrections_;
600 if (eFep_ == FreeEnergyPerturbationType::No)
602 avcsix = topParams_.avcsix_[0];
603 avctwelve = topParams_.avctwelve_[0];
607 avcsix = (1 - lambda) * topParams_.avcsix_[0] + lambda * topParams_.avcsix_[1];
608 avctwelve = (1 - lambda) * topParams_.avctwelve_[0] + lambda * topParams_.avctwelve_[1];
611 const real enerdiff = numCorr * (density * iParams_.enerdiffsix_ - iParams_.enershiftsix_);
612 corr.energy += avcsix * enerdiff;
614 if (eFep_ != FreeEnergyPerturbationType::No)
616 dvdlambda += (topParams_.avcsix_[1] - topParams_.avcsix_[0]) * enerdiff;
620 const real enerdiff = numCorr * (density * iParams_.enerdifftwelve_ - iParams_.enershifttwelve_);
621 corr.energy += avctwelve * enerdiff;
622 if (eFep_ != FreeEnergyPerturbationType::No)
624 dvdlambda += (topParams_.avctwelve_[1] - topParams_.avctwelve_[0]) * enerdiff;
630 corr.virial = numCorr * density * avcsix * iParams_.virdiffsix_ / 3.0;
631 if (eDispCorr_ == DispersionCorrectionType::AllEnerPres)
633 corr.virial += numCorr * density * avctwelve * iParams_.virdifftwelve_ / 3.0;
635 /* The factor 2 is because of the Gromacs virial definition */
636 corr.pressure = -2.0 * invvol * corr.virial * gmx::c_presfac;
639 if (eFep_ != FreeEnergyPerturbationType::No)
641 corr.dvdl += dvdlambda;