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37 * \brief Implements functions for generating update groups
39 * \author Berk Hess <hess@kth.se>
40 * \ingroup module_mdlib
45 #include "updategroups.h"
49 #include <unordered_map>
51 #include "gromacs/math/functions.h"
52 #include "gromacs/math/units.h"
53 #include "gromacs/mdlib/constr.h"
54 #include "gromacs/mdtypes/inputrec.h"
55 #include "gromacs/topology/idef.h"
56 #include "gromacs/topology/ifunc.h"
57 #include "gromacs/topology/topology.h"
58 #include "gromacs/utility/listoflists.h"
63 /*! \brief Returns whether \p moltype contains flexible constraints */
64 static bool hasFlexibleConstraints(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
66 for (auto& ilist : extractILists(moltype.ilist, IF_CONSTRAINT))
68 if (ilist.functionType != F_SETTLE)
70 for (size_t i = 0; i < ilist.iatoms.size(); i += ilistStride(ilist))
72 if (isConstraintFlexible(iparams.data(), ilist.iatoms[i]))
83 /*! \brief Returns whether moltype has incompatible vsites.
85 * For simplicity the only compatible vsites are linear 2 or 3 atom sites
86 * that are constructed in between the 2 or 3 contructing atoms,
88 static bool hasIncompatibleVsites(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
90 bool hasIncompatibleVsites = false;
92 for (auto& ilist : extractILists(moltype.ilist, IF_VSITE))
94 if (ilist.functionType == F_VSITE2 || ilist.functionType == F_VSITE3)
96 for (size_t i = 0; i < ilist.iatoms.size(); i += ilistStride(ilist))
98 const t_iparams& iparam = iparams[ilist.iatoms[i]];
101 if (ilist.functionType == F_VSITE2)
103 coeffMin = iparam.vsite.a;
104 coeffSum = iparam.vsite.a;
108 coeffMin = std::min(iparam.vsite.a, iparam.vsite.b);
109 coeffSum = iparam.vsite.a + iparam.vsite.b;
111 if (coeffMin < 0 || coeffSum > 1)
113 hasIncompatibleVsites = true;
120 hasIncompatibleVsites = true;
125 return hasIncompatibleVsites;
128 /*! \brief Returns a merged list with constraints of all types */
129 static InteractionList jointConstraintList(const gmx_moltype_t& moltype)
131 InteractionList ilistCombined;
132 std::vector<int>& iatoms = ilistCombined.iatoms;
134 for (auto& ilist : extractILists(moltype.ilist, IF_CONSTRAINT))
136 if (ilist.functionType == F_SETTLE)
138 for (size_t i = 0; i < ilist.iatoms.size(); i += ilistStride(ilist))
140 iatoms.push_back(-1);
141 iatoms.push_back(ilist.iatoms[i + 1]);
142 iatoms.push_back(ilist.iatoms[i + 2]);
143 iatoms.push_back(-1);
144 iatoms.push_back(ilist.iatoms[i + 1]);
145 iatoms.push_back(ilist.iatoms[i + 3]);
146 iatoms.push_back(-1);
147 iatoms.push_back(ilist.iatoms[i + 2]);
148 iatoms.push_back(ilist.iatoms[i + 3]);
153 GMX_RELEASE_ASSERT(NRAL(ilist.functionType) == 2,
154 "Can only handle two-atom non-SETTLE constraints");
156 iatoms.insert(iatoms.end(), ilist.iatoms.begin(), ilist.iatoms.end());
160 return ilistCombined;
163 /*! \brief Struct for returning an atom range */
164 struct AtomIndexExtremes
166 int minAtom; //!< The minimum atom index
167 int maxAtom; //!< The maximum atom index
170 /*! \brief Returns the range of constructing atom for vsite with atom index \p a */
171 static AtomIndexExtremes vsiteConstructRange(int a, const gmx_moltype_t& moltype)
173 AtomIndexExtremes extremes = { -1, -1 };
175 for (auto& ilist : extractILists(moltype.ilist, IF_VSITE))
177 for (size_t i = 0; i < ilist.iatoms.size(); i += ilistStride(ilist))
179 if (ilist.iatoms[i + 1] == a)
181 extremes.minAtom = ilist.iatoms[i + 2];
182 extremes.maxAtom = ilist.iatoms[i + 2];
183 for (size_t j = i + 3; j < i + ilistStride(ilist); j++)
185 extremes.minAtom = std::min(extremes.minAtom, ilist.iatoms[j]);
186 extremes.maxAtom = std::max(extremes.maxAtom, ilist.iatoms[j]);
193 GMX_RELEASE_ASSERT(false, "If a is a vsite, we should have found constructing atoms");
198 /*! \brief Returns the range of atoms constrained to atom \p a (including \p a itself) */
199 static AtomIndexExtremes constraintAtomRange(int a,
200 const ListOfLists<int>& at2con,
201 const InteractionList& ilistConstraints)
203 AtomIndexExtremes extremes = { a, a };
205 for (const int constraint : at2con[a])
207 for (int j = 0; j < 2; j++)
209 int atomJ = ilistConstraints.iatoms[constraint * 3 + 1 + j];
210 extremes.minAtom = std::min(extremes.minAtom, atomJ);
211 extremes.maxAtom = std::max(extremes.maxAtom, atomJ);
218 /*! \brief Returns a list that tells whether atoms in \p moltype are vsites */
219 static std::vector<bool> buildIsParticleVsite(const gmx_moltype_t& moltype)
221 std::vector<bool> isVsite(moltype.atoms.nr);
223 for (auto& ilist : extractILists(moltype.ilist, IF_VSITE))
225 for (size_t i = 0; i < ilist.iatoms.size(); i += ilistStride(ilist))
227 int vsiteAtom = ilist.iatoms[i + 1];
228 isVsite[vsiteAtom] = true;
235 /*! \brief Returns the size of the update group starting at \p firstAtom or 0 when criteria (see updategroups.h) are not met */
236 static int detectGroup(int firstAtom,
237 const gmx_moltype_t& moltype,
238 const ListOfLists<int>& at2con,
239 const InteractionList& ilistConstraints)
241 /* We should be using moltype.atoms.atom[].ptype for checking whether
242 * a particle is a vsite. But the test code can't fill t_atoms,
243 * because it uses C pointers which get double freed.
245 std::vector<bool> isParticleVsite = buildIsParticleVsite(moltype);
247 /* A non-vsite atom without constraints is an update group by itself */
248 if (!isParticleVsite[firstAtom] && at2con[firstAtom].empty())
253 /* A (potential) update group starts at firstAtom and should consist
254 * of two or more atoms and possibly vsites. At least one atom should
255 * have constraints with all other atoms and vsites should have all
256 * constructing atoms inside the group. Here we increase lastAtom until
257 * the criteria are fulfilled or exit when criteria cannot be met.
259 int numAtomsWithConstraints = 0;
260 int maxConstraintsPerAtom = 0;
261 int lastAtom = firstAtom;
263 while (a <= lastAtom)
265 if (isParticleVsite[a])
267 AtomIndexExtremes extremes = vsiteConstructRange(a, moltype);
268 if (extremes.minAtom < firstAtom)
270 /* A constructing atom is outside the group,
271 * we can not use update groups.
275 lastAtom = std::max(lastAtom, extremes.maxAtom);
279 const int numConstraints = at2con[a].ssize();
280 if (numConstraints == 0)
282 /* We can not have unconstrained atoms in an update group */
285 /* This atom has at least one constraint.
286 * Check whether all constraints are within the group
287 * and whether we need to extend the group.
289 numAtomsWithConstraints += 1;
290 maxConstraintsPerAtom = std::max(maxConstraintsPerAtom, numConstraints);
292 AtomIndexExtremes extremes = constraintAtomRange(a, at2con, ilistConstraints);
293 if (extremes.minAtom < firstAtom)
295 /* Constraint to atom outside the "group" */
298 lastAtom = std::max(lastAtom, extremes.maxAtom);
304 /* lastAtom might be followed by a vsite that is constructed from atoms
305 * with index <= lastAtom. Handle this case.
307 if (lastAtom + 1 < moltype.atoms.nr && isParticleVsite[lastAtom + 1])
309 AtomIndexExtremes extremes = vsiteConstructRange(lastAtom + 1, moltype);
310 if (extremes.minAtom < firstAtom)
312 /* Constructing atom precedes the group */
315 else if (extremes.maxAtom <= lastAtom)
317 /* All constructing atoms are in the group, add the vsite to the group */
320 else if (extremes.minAtom <= lastAtom)
322 /* Some, but not all constructing atoms are in the group */
327 GMX_RELEASE_ASSERT(maxConstraintsPerAtom < numAtomsWithConstraints,
328 "We have checked that atoms are only constrained to atoms within the group,"
329 "so each atom should have fewer constraints than the number of atoms");
330 /* Check that at least one atom is constrained to all others */
331 if (maxConstraintsPerAtom != numAtomsWithConstraints - 1)
336 return lastAtom - firstAtom + 1;
339 /*! \brief Returns a list of update groups for \p moltype */
340 static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
342 RangePartitioning groups;
344 /* Update groups are not compatible with flexible constraints.
345 * Without dynamics the flexible constraints are ignored,
346 * but since performance for EM/NM is less critical, we do not
347 * use update groups to keep the code here simpler.
349 if (hasFlexibleConstraints(moltype, iparams) || hasIncompatibleVsites(moltype, iparams))
354 /* Combine all constraint ilists into a single one */
355 InteractionList constraintsCombined = jointConstraintList(moltype);
356 t_ilist ilistsCombined[F_NRE];
357 ilistsCombined[F_CONSTR].nr = constraintsCombined.iatoms.size();
358 ilistsCombined[F_CONSTR].iatoms = constraintsCombined.iatoms.data();
359 ilistsCombined[F_CONSTRNC].nr = 0;
360 /* We "include" flexible constraints, but none are present (checked above) */
361 const ListOfLists<int> at2con = make_at2con(moltype.atoms.nr, ilistsCombined, iparams.data(),
362 FlexibleConstraintTreatment::Include);
364 bool satisfiesCriteria = true;
367 while (satisfiesCriteria && firstAtom < moltype.atoms.nr)
369 int numAtomsInGroup = detectGroup(firstAtom, moltype, at2con, constraintsCombined);
371 if (numAtomsInGroup == 0)
373 satisfiesCriteria = false;
377 groups.appendBlock(numAtomsInGroup);
379 firstAtom += numAtomsInGroup;
382 if (!satisfiesCriteria)
384 /* Make groups empty, to signal not satisfying the criteria */
391 std::vector<RangePartitioning> makeUpdateGroups(const gmx_mtop_t& mtop)
393 std::vector<RangePartitioning> updateGroups;
395 bool systemSatisfiesCriteria = true;
396 for (const gmx_moltype_t& moltype : mtop.moltype)
398 updateGroups.push_back(makeUpdateGroups(moltype, mtop.ffparams.iparams));
400 if (updateGroups.back().numBlocks() == 0)
402 systemSatisfiesCriteria = false;
406 if (!systemSatisfiesCriteria)
408 updateGroups.clear();
414 /*! \brief Returns a map of angles ilist.iatoms indices with the middle atom as key */
415 static std::unordered_multimap<int, int> getAngleIndices(const gmx_moltype_t& moltype)
417 const InteractionList& angles = moltype.ilist[F_ANGLES];
419 std::unordered_multimap<int, int> indices(angles.size());
421 for (int i = 0; i < angles.size(); i += 1 + NRAL(F_ANGLES))
423 indices.insert({ angles.iatoms[i + 2], i });
429 /*! \brief When possible, computes the maximum radius of constrained atom in an update group
431 * Supports groups with 2 or 3 atoms where all partner atoms are connected to
432 * each other by angle potentials. The temperature is used to compute a radius
433 * that is not exceeded with a chance of 10^-9. Note that this computation
434 * assumes there are no other strong forces working on these angular
435 * degrees of freedom.
436 * The return value is -1 when all partners are not connected to each other
437 * by one angle potential, when a potential is perturbed or when an angle
438 * could reach more than 180 degrees.
440 template<int numPartnerAtoms>
441 static real constraintGroupRadius(const gmx_moltype_t& moltype,
442 gmx::ArrayRef<const t_iparams> iparams,
443 const int centralAtom,
444 const ListOfLists<int>& at2con,
445 const std::unordered_multimap<int, int>& angleIndices,
446 const real constraintLength,
447 const real temperature)
449 const int numConstraints = at2con[centralAtom].ssize();
450 GMX_RELEASE_ASSERT(numConstraints == numPartnerAtoms,
451 "We expect as many constraints as partner atoms here");
453 std::array<int, numPartnerAtoms> partnerAtoms;
454 for (int i = 0; i < numPartnerAtoms; i++)
456 const int ind = at2con[centralAtom][i] * 3;
457 if (ind >= moltype.ilist[F_CONSTR].size())
459 /* This is a flexible constraint, we don't optimize for that */
462 const int a1 = moltype.ilist[F_CONSTR].iatoms[ind + 1];
463 const int a2 = moltype.ilist[F_CONSTR].iatoms[ind + 2];
464 partnerAtoms[i] = (a1 == centralAtom ? a2 : a1);
467 const InteractionList& angles = moltype.ilist[F_ANGLES];
468 auto range = angleIndices.equal_range(centralAtom);
470 std::array<int, numPartnerAtoms> numAngles = { 0 };
471 bool areSameType = true;
472 for (auto it = range.first; it != range.second; ++it)
474 /* Check if the outer atoms in the angle are both partner atoms */
475 int numAtomsFound = 0;
476 for (int ind = it->second + 1; ind < it->second + 4; ind += 2)
478 for (const int& partnerAtom : partnerAtoms)
480 if (angles.iatoms[ind] == partnerAtom)
486 if (numAtomsFound == 2)
488 /* Check that the angle potentials have the same type */
491 angleType = angles.iatoms[it->second];
493 else if (angles.iatoms[it->second] != angleType)
497 /* Count the number of angle interactions per atoms */
498 for (int ind = it->second + 1; ind < it->second + 4; ind += 2)
500 for (size_t i = 0; i < partnerAtoms.size(); i++)
502 if (angles.iatoms[ind] == partnerAtoms[i])
511 bool criteriaSatisfied = areSameType;
512 for (int i = 0; i < numPartnerAtoms; i++)
514 if (numAngles[i] != numPartnerAtoms - 1)
516 criteriaSatisfied = false;
520 /* We don't bother optimizing the perturbed angle case */
521 const t_iparams& angleParams = iparams[angleType];
522 if (criteriaSatisfied && angleParams.harmonic.rB == angleParams.harmonic.rA
523 && angleParams.harmonic.krB == angleParams.harmonic.krA)
525 /* Set number of stddevs such that change of exceeding < 10^-9 */
526 constexpr real c_numSigma = 6.0;
527 /* Compute the maximally stretched angle */
528 const real eqAngle = angleParams.harmonic.rA * DEG2RAD;
529 const real fc = angleParams.harmonic.krA;
530 const real maxAngle = eqAngle + c_numSigma * BOLTZ * temperature / ((numPartnerAtoms - 1) * fc);
531 if (maxAngle >= M_PI)
536 if (numPartnerAtoms == 2)
538 /* With two atoms constrainted to a cental atom we have a triangle
539 * with two equal sides because the constraint type is equal.
540 * Return the distance from the COG to the farthest two corners,
541 * i.e. the partner atoms.
543 real distMidPartner = std::sin(0.5 * maxAngle) * constraintLength;
544 real distCentralMid = std::cos(0.5 * maxAngle) * constraintLength;
545 real distCogMid = distCentralMid * numPartnerAtoms / (numPartnerAtoms + 1);
546 real distCogPartner = std::sqrt(gmx::square(distMidPartner) + gmx::square(distCogMid));
548 return distCogPartner;
550 else if (numPartnerAtoms == 3)
552 /* With three atoms constrainted to a cental atom we have the
553 * largest COG-atom distance when one partner atom (the outlier)
554 * moves out by stretching its two angles by an equal amount.
555 * The math here gets a bit more involved, but it is still
556 * rather straightforward geometry.
557 * We first compute distances in the plane of the three partners.
558 * Here we have two "equilibrium" partners and one outlier.
559 * We make use of the "Mid" point between the two "Eq" partners.
560 * We project the central atom on this plane.
561 * Then we compute the distance of the central atom to the plane.
562 * The distance of the COG to the ourlier is returned.
564 real halfDistEqPartner = std::sin(0.5 * eqAngle) * constraintLength;
565 real distPartnerOutlier = 2 * std::sin(0.5 * maxAngle) * constraintLength;
566 real distMidOutlier =
567 std::sqrt(gmx::square(distPartnerOutlier) - gmx::square(halfDistEqPartner));
568 real distMidCenterInPlane =
569 0.5 * (distMidOutlier - gmx::square(halfDistEqPartner) / distMidOutlier);
570 real distCentralToPlane =
571 std::sqrt(gmx::square(constraintLength) - gmx::square(halfDistEqPartner)
572 - gmx::square(distMidCenterInPlane));
573 real distCogOutlierH = distCentralToPlane / (numPartnerAtoms + 1);
574 real distCogOutlierP =
575 distMidOutlier - (distMidOutlier + distMidCenterInPlane) / (numPartnerAtoms + 1);
576 real distCogOutlier = std::sqrt(gmx::square(distCogOutlierH) + gmx::square(distCogOutlierP));
578 return distCogOutlier;
582 GMX_RELEASE_ASSERT(false, "Only 2 or 3 constraints are supported here");
589 /*! \brief Returns the maximum update group radius for \p moltype */
590 static real computeMaxUpdateGroupRadius(const gmx_moltype_t& moltype,
591 gmx::ArrayRef<const t_iparams> iparams,
592 const RangePartitioning& updateGroups,
595 GMX_RELEASE_ASSERT(!hasFlexibleConstraints(moltype, iparams),
596 "Flexible constraints are not supported here");
598 const InteractionList& settles = moltype.ilist[F_SETTLE];
600 const ListOfLists<int> at2con = make_at2con(moltype, iparams, FlexibleConstraintTreatment::Include);
602 const auto angleIndices = getAngleIndices(moltype);
605 for (int group = 0; group < updateGroups.numBlocks(); group++)
607 if (updateGroups.block(group).size() == 1)
609 /* Single atom group, radius is zero */
613 /* Find the atom maxAtom with the maximum number of constraints */
614 int maxNumConstraints = 0;
616 for (int a : updateGroups.block(group))
618 const int numConstraints = at2con[a].ssize();
619 if (numConstraints > maxNumConstraints)
621 maxNumConstraints = numConstraints;
625 GMX_ASSERT(maxAtom >= 0 || settles.size() > 0,
626 "We should have at least two atoms in the group with constraints");
632 bool allTypesAreEqual = true;
633 int constraintType = -1;
634 real maxConstraintLength = 0;
635 real sumConstraintLengths = 0;
636 bool isFirstConstraint = true;
637 for (const int constraint : at2con[maxAtom])
639 int conIndex = constraint * (1 + NRAL(F_CONSTR));
641 if (conIndex < moltype.ilist[F_CONSTR].size())
643 iparamsIndex = moltype.ilist[F_CONSTR].iatoms[conIndex];
648 moltype.ilist[F_CONSTRNC].iatoms[conIndex - moltype.ilist[F_CONSTR].size()];
650 if (isFirstConstraint)
652 constraintType = iparamsIndex;
653 isFirstConstraint = false;
655 else if (iparamsIndex != constraintType)
657 allTypesAreEqual = false;
659 /* Here we take the maximum constraint length of the A and B
660 * topology, which assumes lambda is between 0 and 1 for
663 real constraintLength =
664 std::max(iparams[iparamsIndex].constr.dA, iparams[iparamsIndex].constr.dB);
665 maxConstraintLength = std::max(maxConstraintLength, constraintLength);
666 sumConstraintLengths += constraintLength;
669 int numConstraints = at2con[maxAtom].ssize();
671 if (numConstraints == 1)
673 /* Single constraint: the radius is the distance from the midpoint */
674 radius = 0.5_real * maxConstraintLength;
680 /* With 2 constraints the maximum possible radius is the
681 * constraint length, so we can use that for the 0 K case.
683 if (numConstraints == 2 && allTypesAreEqual && temperature > 0)
685 radius = constraintGroupRadius<2>(moltype, iparams, maxAtom, at2con, angleIndices,
686 maxConstraintLength, temperature);
688 /* With 3 constraints the maximum possible radius is 1.4 times
689 * the constraint length, so it is worth computing a smaller
690 * radius to enable update groups for systems in a small box.
692 if (numConstraints == 3 && allTypesAreEqual && temperature >= 0)
694 radius = constraintGroupRadius<3>(moltype, iparams, maxAtom, at2con, angleIndices,
695 maxConstraintLength, temperature);
696 if (temperature == 0 && radius >= 0)
698 /* Add a 10% margin for deviation at 0 K */
705 /* Worst case: atom with the longest constraint on one side
706 * of the center, all others on the opposite side
708 radius = maxConstraintLength
709 + (sumConstraintLengths - 2 * maxConstraintLength) / (numConstraints + 1);
712 maxRadius = std::max(maxRadius, radius);
715 for (int i = 0; i < settles.size(); i += 1 + NRAL(F_SETTLE))
717 const real dOH = iparams[settles.iatoms[i]].settle.doh;
718 const real dHH = iparams[settles.iatoms[i]].settle.dhh;
719 /* Compute distance^2 from center of geometry to O and H */
720 const real dCO2 = (4 * dOH * dOH - dHH * dHH) / 9;
721 const real dCH2 = (dOH * dOH + 2 * dHH * dHH) / 9;
722 const real dCAny = std::sqrt(std::max(dCO2, dCH2));
723 maxRadius = std::max(maxRadius, dCAny);
729 real computeMaxUpdateGroupRadius(const gmx_mtop_t& mtop,
730 gmx::ArrayRef<const RangePartitioning> updateGroups,
733 if (updateGroups.empty())
738 GMX_RELEASE_ASSERT(updateGroups.size() == mtop.moltype.size(),
739 "We need one update group entry per moleculetype");
743 for (size_t moltype = 0; moltype < mtop.moltype.size(); moltype++)
745 maxRadius = std::max(
746 maxRadius, computeMaxUpdateGroupRadius(mtop.moltype[moltype], mtop.ffparams.iparams,
747 updateGroups[moltype], temperature));