2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
7 * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
9 * and including many others, as listed in the AUTHORS file in the
10 * top-level source directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
40 #include "vsite_parm.h"
48 #include "gromacs/gmxpreprocess/add_par.h"
49 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
50 #include "gromacs/gmxpreprocess/grompp_impl.h"
51 #include "gromacs/gmxpreprocess/notset.h"
52 #include "gromacs/gmxpreprocess/toputil.h"
53 #include "gromacs/math/functions.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdtypes/md_enums.h"
57 #include "gromacs/topology/ifunc.h"
58 #include "gromacs/topology/topology.h"
59 #include "gromacs/utility/arrayref.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/gmxassert.h"
63 #include "gromacs/utility/logger.h"
64 #include "gromacs/utility/smalloc.h"
65 #include "gromacs/utility/strconvert.h"
67 #include "hackblock.h"
71 * Data type to store information about bonded interactions for virtual sites.
73 class VsiteBondedInteraction
76 //! Constructor initializes datastructure.
77 VsiteBondedInteraction(gmx::ArrayRef<const int> atomIndex, real parameterValue) :
78 parameterValue_(parameterValue)
80 GMX_RELEASE_ASSERT(atomIndex.size() <= atomIndex_.size(),
81 "Cannot add more atom indices than maximum number");
82 auto atomIndexIt = atomIndex_.begin();
83 for (const auto index : atomIndex)
85 *atomIndexIt++ = index;
89 //! Access the individual elements set for the vsite bonded interaction.
90 const int& ai() const { return atomIndex_[0]; }
91 const int& aj() const { return atomIndex_[1]; }
92 const int& ak() const { return atomIndex_[2]; }
93 const int& al() const { return atomIndex_[3]; }
95 const real& parameterValue() const { return parameterValue_; }
99 //! The distance value for this bonded interaction.
100 real parameterValue_;
101 //! Array of atom indices
102 std::array<int, 4> atomIndex_;
106 * Stores information about single virtual site bonded parameter.
108 struct VsiteBondParameter
110 //! Constructor initializes datastructure.
111 VsiteBondParameter(int ftype, const InteractionOfType& vsiteInteraction) :
113 vsiteInteraction_(vsiteInteraction)
116 //! Function type for virtual site.
119 * Interaction type data.
121 * The datastructure should never be used in a case where the InteractionType
122 * used to construct it might go out of scope before this object, as it would cause
123 * the reference to type_ to dangle.
125 const InteractionOfType& vsiteInteraction_;
129 * Helper type for conversion of bonded parameters to virtual sites.
131 struct Atom2VsiteBond
133 //! Function type for conversion.
135 //! The vsite parameters in a list.
136 std::vector<VsiteBondParameter> vSiteBondedParameters;
139 //! Convenience type def for virtual site connections.
140 using Atom2VsiteConnection = std::vector<int>;
142 static int vsite_bond_nrcheck(int ftype)
146 if ((interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT | IF_ATYPE)) || (ftype == F_IDIHS))
148 nrcheck = NRAL(ftype);
158 static void enter_bonded(int nratoms, std::vector<VsiteBondedInteraction>* bondeds, const InteractionOfType& type)
160 GMX_RELEASE_ASSERT(nratoms == type.atoms().ssize(), "Size of atom array must match");
161 bondeds->emplace_back(VsiteBondedInteraction(type.atoms(), type.c0()));
165 * Wraps the datastructures for the different vsite bondeds.
167 struct AllVsiteBondedInteractions
170 std::vector<VsiteBondedInteraction> bonds;
172 std::vector<VsiteBondedInteraction> angles;
174 std::vector<VsiteBondedInteraction> dihedrals;
177 static AllVsiteBondedInteractions createVsiteBondedInformation(int nrat,
178 gmx::ArrayRef<const int> atoms,
179 gmx::ArrayRef<const Atom2VsiteBond> at2vb)
181 AllVsiteBondedInteractions allVsiteBondeds;
182 for (int k = 0; k < nrat; k++)
184 for (auto& vsite : at2vb[atoms[k]].vSiteBondedParameters)
186 int ftype = vsite.ftype_;
187 const InteractionOfType& type = vsite.vsiteInteraction_;
188 int nrcheck = vsite_bond_nrcheck(ftype);
189 /* abuse nrcheck to see if we're adding bond, angle or idih */
192 case 2: enter_bonded(nrcheck, &allVsiteBondeds.bonds, type); break;
193 case 3: enter_bonded(nrcheck, &allVsiteBondeds.angles, type); break;
194 case 4: enter_bonded(nrcheck, &allVsiteBondeds.dihedrals, type); break;
198 return allVsiteBondeds;
201 static std::vector<Atom2VsiteBond> make_at2vsitebond(int natoms, gmx::ArrayRef<InteractionsOfType> plist)
205 std::vector<Atom2VsiteBond> at2vb(natoms);
208 for (int ftype = 0; (ftype < F_NRE); ftype++)
210 if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN)
212 for (int i = 0; (i < gmx::ssize(plist[ftype])); i++)
214 gmx::ArrayRef<const int> atoms = plist[ftype].interactionTypes[i].atoms();
215 for (int j = 0; j < NRAL(ftype); j++)
217 bVSI[atoms[j]] = TRUE;
223 for (int ftype = 0; (ftype < F_NRE); ftype++)
225 int nrcheck = vsite_bond_nrcheck(ftype);
228 for (int i = 0; (i < gmx::ssize(plist[ftype])); i++)
230 gmx::ArrayRef<const int> aa = plist[ftype].interactionTypes[i].atoms();
231 for (int j = 0; j < nrcheck; j++)
235 at2vb[aa[j]].vSiteBondedParameters.emplace_back(
236 ftype, plist[ftype].interactionTypes[i]);
247 static std::vector<Atom2VsiteConnection> make_at2vsitecon(int natoms, gmx::ArrayRef<InteractionsOfType> plist)
249 std::vector<bool> bVSI(natoms);
250 std::vector<Atom2VsiteConnection> at2vc(natoms);
252 for (int ftype = 0; (ftype < F_NRE); ftype++)
254 if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN)
256 for (int i = 0; (i < gmx::ssize(plist[ftype])); i++)
258 gmx::ArrayRef<const int> atoms = plist[ftype].interactionTypes[i].atoms();
259 for (int j = 0; j < NRAL(ftype); j++)
261 bVSI[atoms[j]] = TRUE;
267 for (int ftype = 0; (ftype < F_NRE); ftype++)
269 if (interaction_function[ftype].flags & IF_CONSTRAINT)
271 for (int i = 0; (i < gmx::ssize(plist[ftype])); i++)
273 int ai = plist[ftype].interactionTypes[i].ai();
274 int aj = plist[ftype].interactionTypes[i].aj();
275 if (bVSI[ai] && bVSI[aj])
277 /* Store forward direction */
278 at2vc[ai].emplace_back(aj);
279 /* Store backward direction */
280 at2vc[aj].emplace_back(ai);
289 static void print_bad(FILE* fp,
290 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
291 gmx::ArrayRef<const VsiteBondedInteraction> angles,
292 gmx::ArrayRef<const VsiteBondedInteraction> idihs)
296 fprintf(fp, "bonds:");
297 for (const auto& bond : bonds)
299 fprintf(fp, " %d-%d (%g)", bond.ai() + 1, bond.aj() + 1, bond.parameterValue());
305 fprintf(fp, "angles:");
306 for (const auto& angle : angles)
308 fprintf(fp, " %d-%d-%d (%g)", angle.ai() + 1, angle.aj() + 1, angle.ak() + 1, angle.parameterValue());
314 fprintf(fp, "idihs:");
315 for (const auto& idih : idihs)
323 idih.parameterValue());
329 static void printInteractionOfType(FILE* fp, int ftype, int i, const InteractionOfType& type)
332 static int prev_ftype = NOTSET;
333 static int prev_i = NOTSET;
335 if ((ftype != prev_ftype) || (i != prev_i))
341 fprintf(fp, "(%d) plist[%s].param[%d]", pass, interaction_function[ftype].name, i);
342 gmx::ArrayRef<const real> forceParam = type.forceParam();
343 for (int j = 0; j < NRFP(ftype); j++)
345 fprintf(fp, ".c[%d]=%g ", j, forceParam[j]);
351 static real get_bond_length(gmx::ArrayRef<const VsiteBondedInteraction> bonds, t_iatom ai, t_iatom aj)
356 for (const auto& bond : bonds)
358 /* check both ways */
359 if (((ai == bond.ai()) && (aj == bond.aj())) || ((ai == bond.aj()) && (aj == bond.ai())))
361 bondlen = bond.parameterValue(); /* note: parameterValue might be NOTSET */
368 static real get_angle(gmx::ArrayRef<const VsiteBondedInteraction> angles, t_iatom ai, t_iatom aj, t_iatom ak)
373 for (const auto& ang : angles)
375 /* check both ways */
376 if (((ai == ang.ai()) && (aj == ang.aj()) && (ak == ang.ak()))
377 || ((ai == ang.ak()) && (aj == ang.aj()) && (ak == ang.ai())))
379 angle = DEG2RAD * ang.parameterValue();
386 static const char* get_atomtype_name_AB(t_atom* atom, PreprocessingAtomTypes* atypes)
388 const char* name = *atypes->atomNameFromAtomType(atom->type);
390 /* When using the decoupling option, atom types are changed
391 * to decoupled for the non-bonded interactions, but the virtual
392 * sites constructions should be based on the "normal" interactions.
393 * So we return the state B atom type name if the state A atom
394 * type is the decoupled one. We should actually check for the atom
395 * type number, but that's not passed here. So we check for
396 * the decoupled atom type name. This should not cause trouble
397 * as this code is only used for topologies with v-sites without
398 * parameters generated by pdb2gmx.
400 if (strcmp(name, "decoupled") == 0)
402 name = *atypes->atomNameFromAtomType(atom->typeB);
408 static bool calc_vsite3_param(PreprocessingAtomTypes* atypes,
409 InteractionOfType* vsite,
411 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
412 gmx::ArrayRef<const VsiteBondedInteraction> angles)
414 /* i = virtual site | ,k
415 * j = 1st bonded heavy atom | i-j
416 * k,l = 2nd bonded atoms | `l
420 real bjk, bjl, a = -1, b = -1;
421 /* check if this is part of a NH3 , NH2-umbrella or CH3 group,
422 * i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
423 bXH3 = ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MNH", 3))
424 && (gmx::equalCaseInsensitive(
425 get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MNH", 3)))
426 || ((gmx::equalCaseInsensitive(
427 get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MCH3", 4))
428 && (gmx::equalCaseInsensitive(
429 get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MCH3", 4)));
431 bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
432 bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
433 bError = (bjk == NOTSET) || (bjl == NOTSET);
436 /* now we get some XH2/XH3 group specific construction */
437 /* note: we call the heavy atom 'C' and the X atom 'N' */
438 real bMM, bCM, bCN, bNH, aCNH, dH, rH, dM, rM;
441 /* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
442 bError = bError || (bjk != bjl);
444 /* the X atom (C or N) in the XH2/XH3 group is the first after the masses: */
445 aN = std::max(vsite->ak(), vsite->al()) + 1;
447 /* get common bonds */
448 bMM = get_bond_length(bonds, vsite->ak(), vsite->al());
450 bCN = get_bond_length(bonds, vsite->aj(), aN);
451 bError = bError || (bMM == NOTSET) || (bCN == NOTSET);
453 /* calculate common things */
455 dM = std::sqrt(gmx::square(bCM) - gmx::square(rM));
457 /* are we dealing with the X atom? */
458 if (vsite->ai() == aN)
460 /* this is trivial */
461 a = b = 0.5 * bCN / dM;
465 /* get other bondlengths and angles: */
466 bNH = get_bond_length(bonds, aN, vsite->ai());
467 aCNH = get_angle(angles, vsite->aj(), aN, vsite->ai());
468 bError = bError || (bNH == NOTSET) || (aCNH == NOTSET);
471 dH = bCN - bNH * std::cos(aCNH);
472 rH = bNH * std::sin(aCNH);
474 a = 0.5 * (dH / dM + rH / rM);
475 b = 0.5 * (dH / dM - rH / rM);
481 "calc_vsite3_param not implemented for the general case "
485 vsite->setForceParameter(0, a);
486 vsite->setForceParameter(1, b);
491 static bool calc_vsite3fd_param(InteractionOfType* vsite,
492 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
493 gmx::ArrayRef<const VsiteBondedInteraction> angles)
495 /* i = virtual site | ,k
496 * j = 1st bonded heavy atom | i-j
497 * k,l = 2nd bonded atoms | `l
501 real bij, bjk, bjl, aijk, aijl, rk, rl;
503 bij = get_bond_length(bonds, vsite->ai(), vsite->aj());
504 bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
505 bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
506 aijk = get_angle(angles, vsite->ai(), vsite->aj(), vsite->ak());
507 aijl = get_angle(angles, vsite->ai(), vsite->aj(), vsite->al());
508 bError = (bij == NOTSET) || (bjk == NOTSET) || (bjl == NOTSET) || (aijk == NOTSET) || (aijl == NOTSET);
510 rk = bjk * std::sin(aijk);
511 rl = bjl * std::sin(aijl);
512 vsite->setForceParameter(0, rk / (rk + rl));
513 vsite->setForceParameter(1, -bij);
518 static bool calc_vsite3fad_param(InteractionOfType* vsite,
519 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
520 gmx::ArrayRef<const VsiteBondedInteraction> angles)
522 /* i = virtual site |
523 * j = 1st bonded heavy atom | i-j
524 * k = 2nd bonded heavy atom | `k-l
525 * l = 3d bonded heavy atom |
528 bool bSwapParity, bError;
531 bSwapParity = (vsite->c1() == -1);
533 bij = get_bond_length(bonds, vsite->ai(), vsite->aj());
534 aijk = get_angle(angles, vsite->ai(), vsite->aj(), vsite->ak());
535 bError = (bij == NOTSET) || (aijk == NOTSET);
537 vsite->setForceParameter(1, bij);
538 vsite->setForceParameter(0, RAD2DEG * aijk);
542 vsite->setForceParameter(0, 360 - vsite->c0());
548 static bool calc_vsite3out_param(PreprocessingAtomTypes* atypes,
549 InteractionOfType* vsite,
551 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
552 gmx::ArrayRef<const VsiteBondedInteraction> angles)
554 /* i = virtual site | ,k
555 * j = 1st bonded heavy atom | i-j
556 * k,l = 2nd bonded atoms | `l
557 * NOTE: i is out of the j-k-l plane!
560 bool bXH3, bError, bSwapParity;
561 real bij, bjk, bjl, aijk, aijl, akjl, pijk, pijl, a, b, c;
563 /* check if this is part of a NH2-umbrella, NH3 or CH3 group,
564 * i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
565 bXH3 = ((gmx::equalCaseInsensitive(get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MNH", 3))
566 && (gmx::equalCaseInsensitive(
567 get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MNH", 3)))
568 || ((gmx::equalCaseInsensitive(
569 get_atomtype_name_AB(&at->atom[vsite->ak()], atypes), "MCH3", 4))
570 && (gmx::equalCaseInsensitive(
571 get_atomtype_name_AB(&at->atom[vsite->al()], atypes), "MCH3", 4)));
573 /* check if construction parity must be swapped */
574 bSwapParity = (vsite->c1() == -1);
576 bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
577 bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
578 bError = (bjk == NOTSET) || (bjl == NOTSET);
581 /* now we get some XH3 group specific construction */
582 /* note: we call the heavy atom 'C' and the X atom 'N' */
583 real bMM, bCM, bCN, bNH, aCNH, dH, rH, rHx, rHy, dM, rM;
586 /* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
587 bError = bError || (bjk != bjl);
589 /* the X atom (C or N) in the XH3 group is the first after the masses: */
590 aN = std::max(vsite->ak(), vsite->al()) + 1;
592 /* get all bondlengths and angles: */
593 bMM = get_bond_length(bonds, vsite->ak(), vsite->al());
595 bCN = get_bond_length(bonds, vsite->aj(), aN);
596 bNH = get_bond_length(bonds, aN, vsite->ai());
597 aCNH = get_angle(angles, vsite->aj(), aN, vsite->ai());
598 bError = bError || (bMM == NOTSET) || (bCN == NOTSET) || (bNH == NOTSET) || (aCNH == NOTSET);
601 dH = bCN - bNH * std::cos(aCNH);
602 rH = bNH * std::sin(aCNH);
603 /* we assume the H's are symmetrically distributed */
604 rHx = rH * std::cos(DEG2RAD * 30);
605 rHy = rH * std::sin(DEG2RAD * 30);
607 dM = std::sqrt(gmx::square(bCM) - gmx::square(rM));
608 a = 0.5 * ((dH / dM) - (rHy / rM));
609 b = 0.5 * ((dH / dM) + (rHy / rM));
610 c = rHx / (2 * dM * rM);
614 /* this is the general construction */
616 bij = get_bond_length(bonds, vsite->ai(), vsite->aj());
617 aijk = get_angle(angles, vsite->ai(), vsite->aj(), vsite->ak());
618 aijl = get_angle(angles, vsite->ai(), vsite->aj(), vsite->al());
619 akjl = get_angle(angles, vsite->ak(), vsite->aj(), vsite->al());
620 bError = bError || (bij == NOTSET) || (aijk == NOTSET) || (aijl == NOTSET) || (akjl == NOTSET);
622 pijk = std::cos(aijk) * bij;
623 pijl = std::cos(aijl) * bij;
624 a = (pijk + (pijk * std::cos(akjl) - pijl) * std::cos(akjl) / gmx::square(std::sin(akjl))) / bjk;
625 b = (pijl + (pijl * std::cos(akjl) - pijk) * std::cos(akjl) / gmx::square(std::sin(akjl))) / bjl;
626 c = -std::sqrt(gmx::square(bij)
627 - (gmx::square(pijk) - 2 * pijk * pijl * std::cos(akjl) + gmx::square(pijl))
628 / gmx::square(std::sin(akjl)))
629 / (bjk * bjl * std::sin(akjl));
632 vsite->setForceParameter(0, a);
633 vsite->setForceParameter(1, b);
636 vsite->setForceParameter(2, -c);
640 vsite->setForceParameter(2, c);
645 static bool calc_vsite4fd_param(InteractionOfType* vsite,
646 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
647 gmx::ArrayRef<const VsiteBondedInteraction> angles,
648 const gmx::MDLogger& logger)
650 /* i = virtual site | ,k
651 * j = 1st bonded heavy atom | i-j-m
652 * k,l,m = 2nd bonded atoms | `l
656 real bij, bjk, bjl, bjm, aijk, aijl, aijm, akjm, akjl;
657 real pk, pl, pm, cosakl, cosakm, sinakl, sinakm, cl, cm;
659 bij = get_bond_length(bonds, vsite->ai(), vsite->aj());
660 bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
661 bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
662 bjm = get_bond_length(bonds, vsite->aj(), vsite->am());
663 aijk = get_angle(angles, vsite->ai(), vsite->aj(), vsite->ak());
664 aijl = get_angle(angles, vsite->ai(), vsite->aj(), vsite->al());
665 aijm = get_angle(angles, vsite->ai(), vsite->aj(), vsite->am());
666 akjm = get_angle(angles, vsite->ak(), vsite->aj(), vsite->am());
667 akjl = get_angle(angles, vsite->ak(), vsite->aj(), vsite->al());
668 bError = (bij == NOTSET) || (bjk == NOTSET) || (bjl == NOTSET) || (bjm == NOTSET) || (aijk == NOTSET)
669 || (aijl == NOTSET) || (aijm == NOTSET) || (akjm == NOTSET) || (akjl == NOTSET);
673 pk = bjk * std::sin(aijk);
674 pl = bjl * std::sin(aijl);
675 pm = bjm * std::sin(aijm);
676 cosakl = (std::cos(akjl) - std::cos(aijk) * std::cos(aijl)) / (std::sin(aijk) * std::sin(aijl));
677 cosakm = (std::cos(akjm) - std::cos(aijk) * std::cos(aijm)) / (std::sin(aijk) * std::sin(aijm));
678 if (cosakl < -1 || cosakl > 1 || cosakm < -1 || cosakm > 1)
680 GMX_LOG(logger.warning)
682 .appendTextFormatted(
683 "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
689 "invalid construction in calc_vsite4fd for atom %d: "
690 "cosakl=%f, cosakm=%f\n",
695 sinakl = std::sqrt(1 - gmx::square(cosakl));
696 sinakm = std::sqrt(1 - gmx::square(cosakm));
698 /* note: there is a '+' because of the way the sines are calculated */
699 cl = -pk / (pl * cosakl - pk + pl * sinakl * (pm * cosakm - pk) / (pm * sinakm));
700 cm = -pk / (pm * cosakm - pk + pm * sinakm * (pl * cosakl - pk) / (pl * sinakl));
702 vsite->setForceParameter(0, cl);
703 vsite->setForceParameter(1, cm);
704 vsite->setForceParameter(2, -bij);
711 static bool calc_vsite4fdn_param(InteractionOfType* vsite,
712 gmx::ArrayRef<const VsiteBondedInteraction> bonds,
713 gmx::ArrayRef<const VsiteBondedInteraction> angles,
714 const gmx::MDLogger& logger)
716 /* i = virtual site | ,k
717 * j = 1st bonded heavy atom | i-j-m
718 * k,l,m = 2nd bonded atoms | `l
722 real bij, bjk, bjl, bjm, aijk, aijl, aijm;
723 real pk, pl, pm, a, b;
725 bij = get_bond_length(bonds, vsite->ai(), vsite->aj());
726 bjk = get_bond_length(bonds, vsite->aj(), vsite->ak());
727 bjl = get_bond_length(bonds, vsite->aj(), vsite->al());
728 bjm = get_bond_length(bonds, vsite->aj(), vsite->am());
729 aijk = get_angle(angles, vsite->ai(), vsite->aj(), vsite->ak());
730 aijl = get_angle(angles, vsite->ai(), vsite->aj(), vsite->al());
731 aijm = get_angle(angles, vsite->ai(), vsite->aj(), vsite->am());
733 bError = (bij == NOTSET) || (bjk == NOTSET) || (bjl == NOTSET) || (bjm == NOTSET)
734 || (aijk == NOTSET) || (aijl == NOTSET) || (aijm == NOTSET);
739 /* Calculate component of bond j-k along the direction i-j */
740 pk = -bjk * std::cos(aijk);
742 /* Calculate component of bond j-l along the direction i-j */
743 pl = -bjl * std::cos(aijl);
745 /* Calculate component of bond j-m along the direction i-j */
746 pm = -bjm * std::cos(aijm);
748 if (fabs(pl) < 1000 * GMX_REAL_MIN || fabs(pm) < 1000 * GMX_REAL_MIN)
750 GMX_LOG(logger.warning)
752 .appendTextFormatted(
753 "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
759 "invalid construction in calc_vsite4fdn for atom %d: "
769 vsite->setForceParameter(0, a);
770 vsite->setForceParameter(1, b);
771 vsite->setForceParameter(2, bij);
778 int set_vsites(bool bVerbose,
780 PreprocessingAtomTypes* atypes,
781 gmx::ArrayRef<InteractionsOfType> plist,
782 const gmx::MDLogger& logger)
791 /* Make a reverse list to avoid ninteractions^2 operations */
792 std::vector<Atom2VsiteBond> at2vb = make_at2vsitebond(atoms->nr, plist);
794 for (ftype = 0; (ftype < F_NRE); ftype++)
796 if (interaction_function[ftype].flags & IF_VSITE)
798 nvsite += plist[ftype].size();
800 if (ftype == F_VSITEN)
802 /* We don't calculate parameters for VSITEN */
808 for (auto& param : plist[ftype].interactionTypes)
810 /* check if all parameters are set */
812 gmx::ArrayRef<const real> forceParam = param.forceParam();
813 for (int j = 0; (j < NRFP(ftype)) && bSet; j++)
815 bSet = forceParam[j] != NOTSET;
820 fprintf(debug, "bSet=%s ", gmx::boolToString(bSet));
821 printInteractionOfType(debug, ftype, i, plist[ftype].interactionTypes[i]);
825 if (bVerbose && bFirst)
829 .appendTextFormatted("Calculating parameters for virtual sites");
834 /* now set the vsite parameters: */
835 AllVsiteBondedInteractions allVsiteBondeds =
836 createVsiteBondedInformation(NRAL(ftype), param.atoms(), at2vb);
840 "Found %zu bonds, %zu angles and %zu idihs "
841 "for virtual site %d (%s)\n",
842 allVsiteBondeds.bonds.size(),
843 allVsiteBondeds.angles.size(),
844 allVsiteBondeds.dihedrals.size(),
846 interaction_function[ftype].longname);
848 allVsiteBondeds.bonds,
849 allVsiteBondeds.angles,
850 allVsiteBondeds.dihedrals);
855 bERROR = calc_vsite3_param(
856 atypes, ¶m, atoms, allVsiteBondeds.bonds, allVsiteBondeds.angles);
859 bERROR = calc_vsite3fd_param(
860 ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles);
863 bERROR = calc_vsite3fad_param(
864 ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles);
867 bERROR = calc_vsite3out_param(
868 atypes, ¶m, atoms, allVsiteBondeds.bonds, allVsiteBondeds.angles);
871 bERROR = calc_vsite4fd_param(
872 ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles, logger);
875 bERROR = calc_vsite4fdn_param(
876 ¶m, allVsiteBondeds.bonds, allVsiteBondeds.angles, logger);
880 "Automatic parameter generation not supported "
882 interaction_function[ftype].longname,
889 "Automatic parameter generation not supported "
890 "for %s atom %d for this bonding configuration",
891 interaction_function[ftype].longname,
902 void set_vsites_ptype(bool bVerbose, gmx_moltype_t* molt, const gmx::MDLogger& logger)
910 .appendTextFormatted("Setting particle type to V for virtual sites");
912 for (ftype = 0; ftype < F_NRE; ftype++)
914 InteractionList* il = &molt->ilist[ftype];
915 if (interaction_function[ftype].flags & IF_VSITE)
917 const int nra = interaction_function[ftype].nratoms;
918 const int nrd = il->size();
919 gmx::ArrayRef<const int> ia = il->iatoms;
925 .appendTextFormatted("doing %d %s virtual sites",
927 interaction_function[ftype].longname);
930 for (i = 0; (i < nrd);)
932 /* The virtual site */
933 int avsite = ia[i + 1];
934 molt->atoms.atom[avsite].ptype = ParticleType::VSite;
943 * Convenience typedef for linking function type to parameter numbers.
945 * The entries in this datastructure are valid if the particle participates in
946 * a virtual site interaction and has a valid vsite function type other than VSITEN.
947 * \todo Change to remove empty constructor when gmx::compat::optional is available.
949 class VsiteAtomMapping
952 //! Only construct with all information in place or nothing
953 VsiteAtomMapping(int functionType, int interactionIndex) :
954 functionType_(functionType),
955 interactionIndex_(interactionIndex)
958 VsiteAtomMapping() : functionType_(-1), interactionIndex_(-1) {}
959 //! Get function type.
960 const int& functionType() const { return functionType_; }
961 //! Get parameter number.
962 const int& interactionIndex() const { return interactionIndex_; }
965 //! Function type for the linked parameter.
967 //! The linked parameter.
968 int interactionIndex_;
971 static void check_vsite_constraints(gmx::ArrayRef<InteractionsOfType> plist,
973 const int vsite_type[],
974 const gmx::MDLogger& logger)
977 for (const auto& param : plist[cftype].interactionTypes)
979 gmx::ArrayRef<const int> atoms = param.atoms();
980 for (int k = 0; k < 2; k++)
983 if (vsite_type[atom] != NOTSET)
987 .appendTextFormatted(
988 "ERROR: Cannot have constraint (%d-%d) with virtual site (%d)",
998 gmx_fatal(FARGS, "There were %d virtual sites involved in constraints", n);
1002 static void clean_vsite_bonds(gmx::ArrayRef<InteractionsOfType> plist,
1003 gmx::ArrayRef<const VsiteAtomMapping> pindex,
1005 const int vsite_type[],
1006 const gmx::MDLogger& logger)
1009 int nconverted, nremoved;
1010 int oatom, at1, at2;
1011 bool bKeep, bRemove, bAllFD;
1012 InteractionsOfType* ps;
1014 if (cftype == F_CONNBONDS)
1019 ps = &(plist[cftype]);
1023 for (auto bond = ps->interactionTypes.begin(); bond != ps->interactionTypes.end();)
1026 const int* first_atoms = nullptr;
1031 /* check if all virtual sites are constructed from the same atoms */
1033 gmx::ArrayRef<const int> atoms = bond->atoms();
1034 for (int k = 0; (k < 2) && !bKeep && !bRemove; k++)
1036 /* for all atoms in the bond */
1037 int atom = atoms[k];
1038 if (vsite_type[atom] != NOTSET && vsite_type[atom] != F_VSITEN)
1041 bool bThisFD = ((pindex[atom].functionType() == F_VSITE3FD)
1042 || (pindex[atom].functionType() == F_VSITE3FAD)
1043 || (pindex[atom].functionType() == F_VSITE4FD)
1044 || (pindex[atom].functionType() == F_VSITE4FDN));
1045 bool bThisOUT = ((pindex[atom].functionType() == F_VSITE3OUT)
1046 && ((interaction_function[cftype].flags & IF_CONSTRAINT) != 0U));
1047 bAllFD = bAllFD && bThisFD;
1048 if (bThisFD || bThisOUT)
1050 oatom = atoms[1 - k]; /* the other atom */
1051 if (vsite_type[oatom] == NOTSET
1053 == plist[pindex[atom].functionType()]
1054 .interactionTypes[pindex[atom].interactionIndex()]
1057 /* if the other atom isn't a vsite, and it is AI */
1067 /* TODO This fragment, and corresponding logic in
1068 clean_vsite_angles and clean_vsite_dihs should
1069 be refactored into a common function */
1072 /* if this is the first vsite we encounter then
1073 store construction atoms */
1074 /* TODO This would be nicer to implement with
1075 a C++ "vector view" class" with an
1076 STL-container-like interface. */
1077 vsnral = NRAL(pindex[atom].functionType()) - 1;
1078 first_atoms = plist[pindex[atom].functionType()]
1079 .interactionTypes[pindex[atom].interactionIndex()]
1086 GMX_ASSERT(vsnral != 0, "nvsite > 1 must have vsnral != 0");
1087 GMX_ASSERT(first_atoms != nullptr,
1088 "nvsite > 1 must have first_atoms != NULL");
1089 /* if it is not the first then
1090 check if this vsite is constructed from the same atoms */
1091 if (vsnral == NRAL(pindex[atom].functionType()) - 1)
1093 for (int m = 0; (m < vsnral) && !bKeep; m++)
1097 bool bPresent = false;
1098 atoms = plist[pindex[atom].functionType()]
1099 .interactionTypes[pindex[atom].interactionIndex()]
1103 for (int n = 0; (n < vsnral) && !bPresent; n++)
1105 if (atoms[m] == first_atoms[n])
1131 /* if we have no virtual sites in this bond, keep it */
1137 /* TODO This loop and the corresponding loop in
1138 check_vsite_angles should be refactored into a common
1140 /* check if all non-vsite atoms are used in construction: */
1141 bool bFirstTwo = true;
1142 for (int k = 0; (k < 2) && !bKeep; k++) /* for all atoms in the bond */
1144 int atom = atoms[k];
1145 if (vsite_type[atom] == NOTSET)
1148 for (int m = 0; (m < vsnral) && !bUsed; m++)
1150 GMX_ASSERT(first_atoms != nullptr,
1151 "If we've seen a vsite before, we know what its first atom "
1154 if (atom == first_atoms[m])
1157 bFirstTwo = bFirstTwo && m < 2;
1167 if (!(bAllFD && bFirstTwo))
1169 /* Two atom bonded interactions include constraints.
1170 * We need to remove constraints between vsite pairs that have
1171 * a fixed distance due to being constructed from the same
1172 * atoms, since this can be numerically unstable.
1174 for (int m = 0; m < vsnral && !bKeep; m++) /* all constr. atoms */
1176 at1 = first_atoms[m];
1177 at2 = first_atoms[(m + 1) % vsnral];
1178 bool bPresent = false;
1179 for (ftype = 0; ftype < F_NRE; ftype++)
1181 if (interaction_function[ftype].flags & IF_CONSTRAINT)
1183 for (auto entry = plist[ftype].interactionTypes.begin();
1184 (entry != plist[ftype].interactionTypes.end()) && !bPresent;
1187 /* all constraints until one matches */
1188 bPresent = (((entry->ai() == at1) && (entry->aj() == at2))
1189 || ((entry->ai() == at2) && (entry->aj() == at1)));
1205 else if (IS_CHEMBOND(cftype))
1207 plist[F_CONNBONDS].interactionTypes.emplace_back(*bond);
1208 bond = ps->interactionTypes.erase(bond);
1213 bond = ps->interactionTypes.erase(bond);
1220 GMX_LOG(logger.info)
1222 .appendTextFormatted("Removed %4d %15ss with virtual sites, %zu left",
1224 interaction_function[cftype].longname,
1229 GMX_LOG(logger.info)
1231 .appendTextFormatted(
1232 "Converted %4d %15ss with virtual sites to connections, %zu left",
1234 interaction_function[cftype].longname,
1239 GMX_LOG(logger.info)
1241 .appendTextFormatted(
1242 "Warning: removed %d %ss with vsite with %s construction\n"
1243 " This vsite construction does not guarantee constant "
1245 " If the constructions were generated by pdb2gmx ignore "
1248 interaction_function[cftype].longname,
1249 interaction_function[F_VSITE3OUT].longname);
1253 static void clean_vsite_angles(gmx::ArrayRef<InteractionsOfType> plist,
1254 gmx::ArrayRef<VsiteAtomMapping> pindex,
1256 const int vsite_type[],
1257 gmx::ArrayRef<const Atom2VsiteConnection> at2vc,
1258 const gmx::MDLogger& logger)
1261 InteractionsOfType* ps;
1263 ps = &(plist[cftype]);
1264 int oldSize = ps->size();
1265 for (auto angle = ps->interactionTypes.begin(); angle != ps->interactionTypes.end();)
1268 const int* first_atoms = nullptr;
1271 bool bAll3FAD = true;
1272 /* check if all virtual sites are constructed from the same atoms */
1274 gmx::ArrayRef<const int> atoms = angle->atoms();
1275 for (int k = 0; (k < 3) && !bKeep; k++) /* for all atoms in the angle */
1277 int atom = atoms[k];
1278 if (vsite_type[atom] != NOTSET && vsite_type[atom] != F_VSITEN)
1281 bAll3FAD = bAll3FAD && (pindex[atom].functionType() == F_VSITE3FAD);
1284 /* store construction atoms of first vsite */
1285 vsnral = NRAL(pindex[atom].functionType()) - 1;
1286 first_atoms = plist[pindex[atom].functionType()]
1287 .interactionTypes[pindex[atom].interactionIndex()]
1294 GMX_ASSERT(vsnral != 0,
1295 "If we've seen a vsite before, we know how many constructing atoms "
1298 first_atoms != nullptr,
1299 "If we've seen a vsite before, we know what its first atom index was");
1300 /* check if this vsite is constructed from the same atoms */
1301 if (vsnral == NRAL(pindex[atom].functionType()) - 1)
1303 for (int m = 0; (m < vsnral) && !bKeep; m++)
1305 const int* subAtoms;
1307 bool bPresent = false;
1308 subAtoms = plist[pindex[atom].functionType()]
1309 .interactionTypes[pindex[atom].interactionIndex()]
1313 for (int n = 0; (n < vsnral) && !bPresent; n++)
1315 if (subAtoms[m] == first_atoms[n])
1334 /* keep all angles with no virtual sites in them or
1335 with virtual sites with more than 3 constr. atoms */
1336 if (nvsite == 0 && vsnral > 3)
1341 /* check if all non-vsite atoms are used in construction: */
1342 bool bFirstTwo = true;
1343 for (int k = 0; (k < 3) && !bKeep; k++) /* for all atoms in the angle */
1346 if (vsite_type[atom] == NOTSET)
1349 for (int m = 0; (m < vsnral) && !bUsed; m++)
1352 first_atoms != nullptr,
1353 "If we've seen a vsite before, we know what its first atom index was");
1355 if (atom == first_atoms[m])
1358 bFirstTwo = bFirstTwo && m < 2;
1368 if (!(bAll3FAD && bFirstTwo))
1370 /* check if all constructing atoms are constrained together */
1371 for (int m = 0; m < vsnral && !bKeep; m++) /* all constr. atoms */
1373 at1 = first_atoms[m];
1374 at2 = first_atoms[(m + 1) % vsnral];
1375 bool bPresent = false;
1376 auto found = std::find(at2vc[at1].begin(), at2vc[at1].end(), at2);
1377 if (found != at2vc[at1].end())
1394 angle = ps->interactionTypes.erase(angle);
1398 if (oldSize != gmx::ssize(*ps))
1400 GMX_LOG(logger.info)
1402 .appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
1403 oldSize - ps->size(),
1404 interaction_function[cftype].longname,
1409 static void clean_vsite_dihs(gmx::ArrayRef<InteractionsOfType> plist,
1410 gmx::ArrayRef<const VsiteAtomMapping> pindex,
1412 const int vsite_type[],
1413 const gmx::MDLogger& logger)
1415 InteractionsOfType* ps;
1417 ps = &(plist[cftype]);
1419 int oldSize = ps->size();
1420 for (auto dih = ps->interactionTypes.begin(); dih != ps->interactionTypes.end();)
1423 const int* first_atoms = nullptr;
1426 gmx::ArrayRef<const int> atoms = dih->atoms();
1428 /* check if all virtual sites are constructed from the same atoms */
1430 for (int k = 0; (k < 4) && !bKeep; k++) /* for all atoms in the dihedral */
1433 if (vsite_type[atom] != NOTSET && vsite_type[atom] != F_VSITEN)
1437 /* store construction atoms of first vsite */
1438 vsnral = NRAL(pindex[atom].functionType()) - 1;
1439 first_atoms = plist[pindex[atom].functionType()]
1440 .interactionTypes[pindex[atom].interactionIndex()]
1447 GMX_ASSERT(vsnral != 0,
1448 "If we've seen a vsite before, we know how many constructing atoms "
1451 first_atoms != nullptr,
1452 "If we've seen a vsite before, we know what its first atom index was");
1453 /* check if this vsite is constructed from the same atoms */
1454 if (vsnral == NRAL(pindex[atom].functionType()) - 1)
1456 for (int m = 0; (m < vsnral) && !bKeep; m++)
1458 const int* subAtoms;
1460 bool bPresent = false;
1461 subAtoms = plist[pindex[atom].functionType()]
1462 .interactionTypes[pindex[atom].interactionIndex()]
1466 for (int n = 0; (n < vsnral) && !bPresent; n++)
1468 if (subAtoms[m] == first_atoms[n])
1480 /* TODO clean_site_bonds and _angles do this increment
1481 at the top of the loop. Refactor this for
1487 /* keep all dihedrals with no virtual sites in them */
1493 /* check if all atoms in dihedral are either virtual sites, or used in
1494 construction of virtual sites. If so, keep it, if not throw away: */
1495 for (int k = 0; (k < 4) && !bKeep; k++) /* for all atoms in the dihedral */
1497 GMX_ASSERT(vsnral != 0,
1498 "If we've seen a vsite before, we know how many constructing atoms it had");
1499 GMX_ASSERT(first_atoms != nullptr,
1500 "If we've seen a vsite before, we know what its first atom index was");
1502 if (vsite_type[atom] == NOTSET)
1504 /* vsnral will be set here, we don't get here with nvsite==0 */
1506 for (int m = 0; (m < vsnral) && !bUsed; m++)
1508 if (atom == first_atoms[m])
1526 dih = ps->interactionTypes.erase(dih);
1530 if (oldSize != gmx::ssize(*ps))
1532 GMX_LOG(logger.info)
1534 .appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
1535 oldSize - ps->size(),
1536 interaction_function[cftype].longname,
1541 // TODO use gmx::compat::optional for pindex.
1542 void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType> plist,
1545 const gmx::MDLogger& logger)
1549 std::vector<VsiteAtomMapping> pindex;
1550 std::vector<Atom2VsiteConnection> at2vc;
1552 /* make vsite_type array */
1553 snew(vsite_type, natoms);
1554 for (int i = 0; i < natoms; i++)
1556 vsite_type[i] = NOTSET;
1559 for (int ftype = 0; ftype < F_NRE; ftype++)
1561 if (interaction_function[ftype].flags & IF_VSITE)
1563 nvsite += plist[ftype].size();
1565 while (i < gmx::ssize(plist[ftype]))
1567 vsite = plist[ftype].interactionTypes[i].ai();
1568 if (vsite_type[vsite] == NOTSET)
1570 vsite_type[vsite] = ftype;
1574 gmx_fatal(FARGS, "multiple vsite constructions for atom %d", vsite + 1);
1576 if (ftype == F_VSITEN)
1578 while (i < gmx::ssize(plist[ftype]) && plist[ftype].interactionTypes[i].ai() == vsite)
1591 /* the rest only if we have virtual sites: */
1594 GMX_LOG(logger.info)
1596 .appendTextFormatted("Cleaning up constraints %swith virtual sites",
1597 bRmVSiteBds ? "and constant bonded interactions " : "");
1599 /* Make a reverse list to avoid ninteractions^2 operations */
1600 at2vc = make_at2vsitecon(natoms, plist);
1602 pindex.resize(natoms);
1603 for (int ftype = 0; ftype < F_NRE; ftype++)
1605 /* Here we skip VSITEN. In neary all practical use cases this
1606 * is not an issue, since VSITEN is intended for constructing
1607 * additional interaction sites, not for replacing normal atoms
1608 * with bonded interactions. Thus we do not expect constant
1609 * bonded interactions. If VSITEN does get used with constant
1610 * bonded interactions, these are not removed which only leads
1611 * to very minor extra computation and constant energy.
1612 * The only problematic case is onstraints between VSITEN
1613 * constructions with fixed distance (which is anyhow useless).
1614 * This will generate a fatal error in check_vsite_constraints.
1616 if ((interaction_function[ftype].flags & IF_VSITE) && ftype != F_VSITEN)
1618 for (gmx::index interactionIndex = 0; interactionIndex < gmx::ssize(plist[ftype]);
1621 int k = plist[ftype].interactionTypes[interactionIndex].ai();
1622 pindex[k] = VsiteAtomMapping(ftype, interactionIndex);
1627 /* remove interactions that include virtual sites */
1628 for (int ftype = 0; ftype < F_NRE; ftype++)
1630 if (((interaction_function[ftype].flags & IF_BOND) && bRmVSiteBds)
1631 || (interaction_function[ftype].flags & IF_CONSTRAINT))
1633 if (interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT))
1635 clean_vsite_bonds(plist, pindex, ftype, vsite_type, logger);
1637 else if (interaction_function[ftype].flags & IF_ATYPE)
1639 clean_vsite_angles(plist, pindex, ftype, vsite_type, at2vc, logger);
1641 else if ((ftype == F_PDIHS) || (ftype == F_IDIHS))
1643 clean_vsite_dihs(plist, pindex, ftype, vsite_type, logger);
1647 /* check that no remaining constraints include virtual sites */
1648 for (int ftype = 0; ftype < F_NRE; ftype++)
1650 if (interaction_function[ftype].flags & IF_CONSTRAINT)
1652 check_vsite_constraints(plist, ftype, vsite_type, logger);