2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2006 - 2014, The GROMACS development team.
5 * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
6 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
7 * and including many others, as listed in the AUTHORS file in the
8 * top-level source directory and at http://www.gromacs.org.
10 * GROMACS is free software; you can redistribute it and/or
11 * modify it under the terms of the GNU Lesser General Public License
12 * as published by the Free Software Foundation; either version 2.1
13 * of the License, or (at your option) any later version.
15 * GROMACS is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 * Lesser General Public License for more details.
20 * You should have received a copy of the GNU Lesser General Public
21 * License along with GROMACS; if not, see
22 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
23 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 * If you want to redistribute modifications to GROMACS, please
26 * consider that scientific software is very special. Version
27 * control is crucial - bugs must be traceable. We will be happy to
28 * consider code for inclusion in the official distribution, but
29 * derived work must not be called official GROMACS. Details are found
30 * in the README & COPYING files - if they are missing, get the
31 * official version at http://www.gromacs.org.
33 * To help us fund GROMACS development, we humbly ask that you cite
34 * the research papers on the package. Check out http://www.gromacs.org.
39 * \brief This file defines functions used by the domdec module
40 * while managing the construction, use and error checking for
41 * topologies local to a DD rank.
43 * \author Berk Hess <hess@kth.se>
44 * \ingroup module_domdec
57 #include "gromacs/domdec/domdec.h"
58 #include "gromacs/domdec/domdec_network.h"
59 #include "gromacs/domdec/ga2la.h"
60 #include "gromacs/gmxlib/chargegroup.h"
61 #include "gromacs/gmxlib/network.h"
62 #include "gromacs/math/vec.h"
63 #include "gromacs/mdlib/forcerec.h"
64 #include "gromacs/mdlib/gmx_omp_nthreads.h"
65 #include "gromacs/mdtypes/commrec.h"
66 #include "gromacs/mdtypes/inputrec.h"
67 #include "gromacs/mdtypes/md_enums.h"
68 #include "gromacs/mdtypes/mdatom.h"
69 #include "gromacs/mdtypes/state.h"
70 #include "gromacs/pbcutil/mshift.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/topology/ifunc.h"
73 #include "gromacs/topology/mtop_util.h"
74 #include "gromacs/topology/topsort.h"
75 #include "gromacs/utility/cstringutil.h"
76 #include "gromacs/utility/exceptions.h"
77 #include "gromacs/utility/fatalerror.h"
78 #include "gromacs/utility/gmxassert.h"
79 #include "gromacs/utility/logger.h"
80 #include "gromacs/utility/smalloc.h"
81 #include "gromacs/utility/strconvert.h"
82 #include "gromacs/utility/stringstream.h"
83 #include "gromacs/utility/stringutil.h"
84 #include "gromacs/utility/textwriter.h"
86 #include "domdec_constraints.h"
87 #include "domdec_internal.h"
88 #include "domdec_vsite.h"
91 /*! \brief The number of integer item in the local state, used for broadcasting of the state */
92 #define NITEM_DD_INIT_LOCAL_STATE 5
94 struct reverse_ilist_t
96 std::vector
<int> index
; /* Index for each atom into il */
97 std::vector
<int> il
; /* ftype|type|a0|...|an|ftype|... */
98 int numAtomsInMolecule
; /* The number of atoms in this molecule */
101 struct MolblockIndices
109 /*! \brief Struct for thread local work data for local topology generation */
112 t_idef idef
; /**< Partial local topology */
113 std::unique_ptr
<VsitePbc
> vsitePbc
; /**< vsite PBC structure */
114 int nbonded
; /**< The number of bondeds in this struct */
115 t_blocka excl
; /**< List of exclusions */
116 int excl_count
; /**< The total exclusion count for \p excl */
119 /*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
120 struct gmx_reverse_top_t
122 //! @cond Doxygen_Suppress
123 //! \brief Do we require all exclusions to be assigned?
124 bool bExclRequired
= false;
125 //! \brief The maximum number of exclusions one atom can have
126 int n_excl_at_max
= 0;
127 //! \brief Are there constraints in this revserse top?
128 bool bConstr
= false;
129 //! \brief Are there settles in this revserse top?
130 bool bSettle
= false;
131 //! \brief All bonded interactions have to be assigned?
132 bool bBCheck
= false;
133 //! \brief Are there bondeds/exclusions between charge-groups?
134 bool bInterCGInteractions
= false;
135 //! \brief Reverse ilist for all moltypes
136 std::vector
<reverse_ilist_t
> ril_mt
;
137 //! \brief The size of ril_mt[?].index summed over all entries
138 int ril_mt_tot_size
= 0;
139 //! \brief The sorting state of bondeds for free energy
140 int ilsort
= ilsortUNKNOWN
;
141 //! \brief molblock to global atom index for quick lookup of molblocks on atom index
142 std::vector
<MolblockIndices
> mbi
;
144 //! \brief Do we have intermolecular interactions?
145 bool bIntermolecularInteractions
= false;
146 //! \brief Intermolecular reverse ilist
147 reverse_ilist_t ril_intermol
;
149 /* Work data structures for multi-threading */
150 //! \brief Thread work array for local topology generation
151 std::vector
<thread_work_t
> th_work
;
155 /*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
156 static int nral_rt(int ftype
)
161 if (interaction_function
[ftype
].flags
& IF_VSITE
)
163 /* With vsites the reverse topology contains an extra entry
164 * for storing if constructing atoms are vsites.
172 /*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
173 static gmx_bool
dd_check_ftype(int ftype
, gmx_bool bBCheck
,
174 gmx_bool bConstr
, gmx_bool bSettle
)
176 return ((((interaction_function
[ftype
].flags
& IF_BOND
) != 0U) &&
177 ((interaction_function
[ftype
].flags
& IF_VSITE
) == 0U) &&
178 (bBCheck
|| ((interaction_function
[ftype
].flags
& IF_LIMZERO
) == 0U))) ||
179 (bConstr
&& (ftype
== F_CONSTR
|| ftype
== F_CONSTRNC
)) ||
180 (bSettle
&& ftype
== F_SETTLE
));
183 /*! \brief Help print error output when interactions are missing */
185 print_missing_interactions_mb(t_commrec
*cr
,
186 const gmx_reverse_top_t
*rt
,
187 const char *moltypename
,
188 const reverse_ilist_t
*ril
,
189 int a_start
, int a_end
,
190 int nat_mol
, int nmol
,
194 int nril_mol
= ril
->index
[nat_mol
];
195 snew(assigned
, nmol
*nril_mol
);
196 gmx::StringOutputStream stream
;
197 gmx::TextWriter
log(&stream
);
199 gmx::ArrayRef
<const int> gatindex
= cr
->dd
->globalAtomIndices
;
200 for (int ftype
= 0; ftype
< F_NRE
; ftype
++)
202 if (dd_check_ftype(ftype
, rt
->bBCheck
, rt
->bConstr
, rt
->bSettle
))
204 int nral
= NRAL(ftype
);
205 const t_ilist
*il
= &idef
->il
[ftype
];
206 const t_iatom
*ia
= il
->iatoms
;
207 for (int i
= 0; i
< il
->nr
; i
+= 1+nral
)
209 int a0
= gatindex
[ia
[1]];
210 /* Check if this interaction is in
211 * the currently checked molblock.
213 if (a0
>= a_start
&& a0
< a_end
)
215 int mol
= (a0
- a_start
)/nat_mol
;
216 int a0_mol
= (a0
- a_start
) - mol
*nat_mol
;
217 int j_mol
= ril
->index
[a0_mol
];
219 while (j_mol
< ril
->index
[a0_mol
+1] && !found
)
221 int j
= mol
*nril_mol
+ j_mol
;
222 int ftype_j
= ril
->il
[j_mol
];
223 /* Here we need to check if this interaction has
224 * not already been assigned, since we could have
225 * multiply defined interactions.
227 if (ftype
== ftype_j
&& ia
[0] == ril
->il
[j_mol
+1] &&
230 /* Check the atoms */
232 for (int a
= 0; a
< nral
; a
++)
234 if (gatindex
[ia
[1+a
]] !=
235 a_start
+ mol
*nat_mol
+ ril
->il
[j_mol
+2+a
])
245 j_mol
+= 2 + nral_rt(ftype_j
);
249 gmx_incons("Some interactions seem to be assigned multiple times");
257 gmx_sumi(nmol
*nril_mol
, assigned
, cr
);
261 for (int mol
= 0; mol
< nmol
; mol
++)
264 while (j_mol
< nril_mol
)
266 int ftype
= ril
->il
[j_mol
];
267 int nral
= NRAL(ftype
);
268 int j
= mol
*nril_mol
+ j_mol
;
269 if (assigned
[j
] == 0 &&
270 !(interaction_function
[ftype
].flags
& IF_VSITE
))
272 if (DDMASTER(cr
->dd
))
276 log
.writeLineFormatted("Molecule type '%s'", moltypename
);
277 log
.writeLineFormatted(
278 "the first %d missing interactions, except for exclusions:", nprint
);
280 log
.writeStringFormatted("%20s atoms",
281 interaction_function
[ftype
].longname
);
283 for (a
= 0; a
< nral
; a
++)
285 log
.writeStringFormatted("%5d", ril
->il
[j_mol
+2+a
]+1);
289 log
.writeString(" ");
292 log
.writeString(" global");
293 for (a
= 0; a
< nral
; a
++)
295 log
.writeStringFormatted("%6d",
296 a_start
+mol
*nat_mol
+ril
->il
[j_mol
+2+a
]+1);
298 log
.ensureLineBreak();
306 j_mol
+= 2 + nral_rt(ftype
);
311 return stream
.toString();
314 /*! \brief Help print error output when interactions are missing */
315 static void print_missing_interactions_atoms(const gmx::MDLogger
&mdlog
,
317 const gmx_mtop_t
*mtop
,
320 const gmx_reverse_top_t
*rt
= cr
->dd
->reverse_top
;
322 /* Print the atoms in the missing interactions per molblock */
324 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
326 const gmx_moltype_t
&moltype
= mtop
->moltype
[molb
.type
];
328 a_end
= a_start
+ molb
.nmol
*moltype
.atoms
.nr
;
330 GMX_LOG(mdlog
.warning
).appendText(
331 print_missing_interactions_mb(cr
, rt
,
333 &rt
->ril_mt
[molb
.type
],
334 a_start
, a_end
, moltype
.atoms
.nr
,
340 void dd_print_missing_interactions(const gmx::MDLogger
&mdlog
,
343 const gmx_mtop_t
*top_global
,
344 const gmx_localtop_t
*top_local
,
348 int ndiff_tot
, cl
[F_NRE
], n
, ndiff
, rest_global
, rest_local
;
354 GMX_LOG(mdlog
.warning
).appendText(
355 "Not all bonded interactions have been properly assigned to the domain decomposition cells");
357 ndiff_tot
= local_count
- dd
->nbonded_global
;
359 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
362 cl
[ftype
] = top_local
->idef
.il
[ftype
].nr
/(1+nral
);
365 gmx_sumi(F_NRE
, cl
, cr
);
369 GMX_LOG(mdlog
.warning
).appendText("A list of missing interactions:");
370 rest_global
= dd
->nbonded_global
;
371 rest_local
= local_count
;
372 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
374 /* In the reverse and local top all constraints are merged
375 * into F_CONSTR. So in the if statement we skip F_CONSTRNC
376 * and add these constraints when doing F_CONSTR.
378 if (((interaction_function
[ftype
].flags
& IF_BOND
) &&
379 (dd
->reverse_top
->bBCheck
380 || !(interaction_function
[ftype
].flags
& IF_LIMZERO
)))
381 || (dd
->reverse_top
->bConstr
&& ftype
== F_CONSTR
)
382 || (dd
->reverse_top
->bSettle
&& ftype
== F_SETTLE
))
384 n
= gmx_mtop_ftype_count(top_global
, ftype
);
385 if (ftype
== F_CONSTR
)
387 n
+= gmx_mtop_ftype_count(top_global
, F_CONSTRNC
);
389 ndiff
= cl
[ftype
] - n
;
392 GMX_LOG(mdlog
.warning
).appendTextFormatted(
393 "%20s of %6d missing %6d",
394 interaction_function
[ftype
].longname
, n
, -ndiff
);
397 rest_local
-= cl
[ftype
];
401 ndiff
= rest_local
- rest_global
;
404 GMX_LOG(mdlog
.warning
).appendTextFormatted(
405 "%20s of %6d missing %6d", "exclusions",
406 rest_global
, -ndiff
);
410 print_missing_interactions_atoms(mdlog
, cr
, top_global
, &top_local
->idef
);
411 write_dd_pdb("dd_dump_err", 0, "dump", top_global
, cr
,
414 std::string errorMessage
;
418 errorMessage
= "One or more interactions were assigned to multiple domains of the domain decompostion. Please report this bug.";
422 errorMessage
= gmx::formatString("%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot
, cr
->dd
->nbonded_global
, dd_cutoff_multibody(dd
), dd_cutoff_twobody(dd
));
424 gmx_fatal_collective(FARGS
, cr
->mpi_comm_mygroup
, MASTER(cr
), "%s", errorMessage
.c_str());
427 /*! \brief Return global topology molecule information for global atom index \p i_gl */
428 static void global_atomnr_to_moltype_ind(const gmx_reverse_top_t
*rt
,
430 int *mb
, int *mt
, int *mol
, int *i_mol
)
432 const MolblockIndices
*mbi
= rt
->mbi
.data();
434 int end
= rt
->mbi
.size(); /* exclusive */
437 /* binary search for molblock_ind */
441 if (i_gl
>= mbi
[mid
].a_end
)
445 else if (i_gl
< mbi
[mid
].a_start
)
459 *mol
= (i_gl
- mbi
->a_start
) / mbi
->natoms_mol
;
460 *i_mol
= (i_gl
- mbi
->a_start
) - (*mol
)*mbi
->natoms_mol
;
463 /*! \brief Count the exclusions for all atoms in \p cgs */
464 static void count_excls(const t_block
*cgs
, const t_blocka
*excls
,
465 int *n_excl
, int *n_intercg_excl
, int *n_excl_at_max
)
467 int cg
, at0
, at1
, at
, excl
, atj
;
472 for (cg
= 0; cg
< cgs
->nr
; cg
++)
474 at0
= cgs
->index
[cg
];
475 at1
= cgs
->index
[cg
+1];
476 for (at
= at0
; at
< at1
; at
++)
478 for (excl
= excls
->index
[at
]; excl
< excls
->index
[at
+1]; excl
++)
480 atj
= excls
->a
[excl
];
484 if (atj
< at0
|| atj
>= at1
)
491 *n_excl_at_max
= std::max(*n_excl_at_max
,
492 excls
->index
[at
+1] - excls
->index
[at
]);
497 /*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
498 static int low_make_reverse_ilist(const InteractionLists
&il_mt
,
501 gmx_bool bConstr
, gmx_bool bSettle
,
503 gmx::ArrayRef
<const int> r_index
,
504 gmx::ArrayRef
<int> r_il
,
505 gmx_bool bLinkToAllAtoms
,
508 int ftype
, j
, nlink
, link
;
513 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
515 if ((interaction_function
[ftype
].flags
& (IF_BOND
| IF_VSITE
)) ||
516 (bConstr
&& (ftype
== F_CONSTR
|| ftype
== F_CONSTRNC
)) ||
517 (bSettle
&& ftype
== F_SETTLE
))
519 const bool bVSite
= ((interaction_function
[ftype
].flags
& IF_VSITE
) != 0U);
520 const int nral
= NRAL(ftype
);
521 const auto &il
= il_mt
[ftype
];
522 for (int i
= 0; i
< il
.size(); i
+= 1+nral
)
524 const int* ia
= il
.iatoms
.data() + i
;
529 /* We don't need the virtual sites for the cg-links */
539 /* Couple to the first atom in the interaction */
542 for (link
= 0; link
< nlink
; link
++)
547 GMX_ASSERT(!r_il
.empty(), "with bAssign not allowed to be empty");
548 GMX_ASSERT(!r_index
.empty(), "with bAssign not allowed to be empty");
549 r_il
[r_index
[a
]+count
[a
]] =
550 (ftype
== F_CONSTRNC
? F_CONSTR
: ftype
);
551 r_il
[r_index
[a
]+count
[a
]+1] = ia
[0];
552 for (j
= 1; j
< 1+nral
; j
++)
554 /* Store the molecular atom number */
555 r_il
[r_index
[a
]+count
[a
]+1+j
] = ia
[j
];
558 if (interaction_function
[ftype
].flags
& IF_VSITE
)
562 /* Add an entry to iatoms for storing
563 * which of the constructing atoms are
566 r_il
[r_index
[a
]+count
[a
]+2+nral
] = 0;
567 for (j
= 2; j
< 1+nral
; j
++)
569 if (atom
[ia
[j
]].ptype
== eptVSite
)
571 r_il
[r_index
[a
]+count
[a
]+2+nral
] |= (2<<j
);
578 /* We do not count vsites since they are always
579 * uniquely assigned and can be assigned
580 * to multiple nodes with recursive vsites.
583 !(interaction_function
[ftype
].flags
& IF_LIMZERO
))
588 count
[a
] += 2 + nral_rt(ftype
);
597 /*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
598 static int make_reverse_ilist(const InteractionLists
&ilist
,
599 const t_atoms
*atoms
,
600 gmx_bool bConstr
, gmx_bool bSettle
,
602 gmx_bool bLinkToAllAtoms
,
603 reverse_ilist_t
*ril_mt
)
605 int nat_mt
, *count
, i
, nint_mt
;
607 /* Count the interactions */
610 low_make_reverse_ilist(ilist
, atoms
->atom
,
612 bConstr
, bSettle
, bBCheck
,
614 bLinkToAllAtoms
, FALSE
);
616 ril_mt
->index
.push_back(0);
617 for (i
= 0; i
< nat_mt
; i
++)
619 ril_mt
->index
.push_back(ril_mt
->index
[i
] + count
[i
]);
622 ril_mt
->il
.resize(ril_mt
->index
[nat_mt
]);
624 /* Store the interactions */
626 low_make_reverse_ilist(ilist
, atoms
->atom
,
628 bConstr
, bSettle
, bBCheck
,
629 ril_mt
->index
, ril_mt
->il
,
630 bLinkToAllAtoms
, TRUE
);
634 ril_mt
->numAtomsInMolecule
= atoms
->nr
;
639 /*! \brief Generate the reverse topology */
640 static gmx_reverse_top_t
make_reverse_top(const gmx_mtop_t
*mtop
, gmx_bool bFE
,
641 gmx_bool bConstr
, gmx_bool bSettle
,
642 gmx_bool bBCheck
, int *nint
)
644 gmx_reverse_top_t rt
;
646 /* Should we include constraints (for SHAKE) in rt? */
647 rt
.bConstr
= bConstr
;
648 rt
.bSettle
= bSettle
;
649 rt
.bBCheck
= bBCheck
;
651 rt
.bInterCGInteractions
= mtop
->bIntermolecularInteractions
;
652 rt
.ril_mt
.resize(mtop
->moltype
.size());
653 rt
.ril_mt_tot_size
= 0;
654 std::vector
<int> nint_mt
;
655 for (size_t mt
= 0; mt
< mtop
->moltype
.size(); mt
++)
657 const gmx_moltype_t
&molt
= mtop
->moltype
[mt
];
660 rt
.bInterCGInteractions
= true;
663 /* Make the atom to interaction list for this molecule type */
664 int numberOfInteractions
=
665 make_reverse_ilist(molt
.ilist
, &molt
.atoms
,
666 rt
.bConstr
, rt
.bSettle
, rt
.bBCheck
, FALSE
,
668 nint_mt
.push_back(numberOfInteractions
);
670 rt
.ril_mt_tot_size
+= rt
.ril_mt
[mt
].index
[molt
.atoms
.nr
];
674 fprintf(debug
, "The total size of the atom to interaction index is %d integers\n", rt
.ril_mt_tot_size
);
678 for (const gmx_molblock_t
&molblock
: mtop
->molblock
)
680 *nint
+= molblock
.nmol
*nint_mt
[molblock
.type
];
683 /* Make an intermolecular reverse top, if necessary */
684 rt
.bIntermolecularInteractions
= mtop
->bIntermolecularInteractions
;
685 if (rt
.bIntermolecularInteractions
)
687 t_atoms atoms_global
;
689 atoms_global
.nr
= mtop
->natoms
;
690 atoms_global
.atom
= nullptr; /* Only used with virtual sites */
692 GMX_RELEASE_ASSERT(mtop
->intermolecular_ilist
, "We should have an ilist when intermolecular interactions are on");
695 make_reverse_ilist(*mtop
->intermolecular_ilist
,
697 rt
.bConstr
, rt
.bSettle
, rt
.bBCheck
, FALSE
,
701 if (bFE
&& gmx_mtop_bondeds_free_energy(mtop
))
703 rt
.ilsort
= ilsortFE_UNSORTED
;
707 rt
.ilsort
= ilsortNO_FE
;
710 /* Make a molblock index for fast searching */
712 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
714 const gmx_molblock_t
&molb
= mtop
->molblock
[mb
];
715 const int numAtomsPerMol
= mtop
->moltype
[molb
.type
].atoms
.nr
;
718 i
+= molb
.nmol
*numAtomsPerMol
;
720 mbi
.natoms_mol
= numAtomsPerMol
;
721 mbi
.type
= molb
.type
;
722 rt
.mbi
.push_back(mbi
);
725 rt
.th_work
.resize(gmx_omp_nthreads_get(emntDomdec
));
730 void dd_make_reverse_top(FILE *fplog
,
731 gmx_domdec_t
*dd
, const gmx_mtop_t
*mtop
,
732 const gmx_vsite_t
*vsite
,
733 const t_inputrec
*ir
, gmx_bool bBCheck
)
737 fprintf(fplog
, "\nLinking all bonded interactions to atoms\n");
740 /* If normal and/or settle constraints act only within charge groups,
741 * we can store them in the reverse top and simply assign them to domains.
742 * Otherwise we need to assign them to multiple domains and set up
743 * the parallel version constraint algorithm(s).
746 dd
->reverse_top
= new gmx_reverse_top_t
;
748 make_reverse_top(mtop
, ir
->efep
!= efepNO
,
749 !dd
->comm
->systemInfo
.haveSplitConstraints
,
750 !dd
->comm
->systemInfo
.haveSplitSettles
,
751 bBCheck
, &dd
->nbonded_global
);
753 gmx_reverse_top_t
*rt
= dd
->reverse_top
;
755 /* With the Verlet scheme, exclusions are handled in the non-bonded
756 * kernels and only exclusions inside the cut-off lead to exclusion
757 * forces. Since each atom pair is treated at most once in the non-bonded
758 * kernels, it doesn't matter if the exclusions for the same atom pair
759 * appear multiple times in the exclusion list.
761 rt
->bExclRequired
= (ir
->cutoff_scheme
== ecutsGROUP
&&
762 inputrecExclForces(ir
));
765 dd
->n_intercg_excl
= 0;
766 rt
->n_excl_at_max
= 0;
767 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
769 int n_excl_mol
, n_excl_icg
, n_excl_at_max
;
771 const gmx_moltype_t
&molt
= mtop
->moltype
[molb
.type
];
772 count_excls(&molt
.cgs
, &molt
.excls
,
773 &n_excl_mol
, &n_excl_icg
, &n_excl_at_max
);
774 nexcl
+= molb
.nmol
*n_excl_mol
;
775 dd
->n_intercg_excl
+= molb
.nmol
*n_excl_icg
;
776 rt
->n_excl_at_max
= std::max(rt
->n_excl_at_max
, n_excl_at_max
);
778 if (rt
->bExclRequired
)
780 dd
->nbonded_global
+= nexcl
;
781 if (EEL_FULL(ir
->coulombtype
) && dd
->n_intercg_excl
> 0 && fplog
)
783 fprintf(fplog
, "There are %d inter charge-group exclusions,\n"
784 "will use an extra communication step for exclusion forces for %s\n",
785 dd
->n_intercg_excl
, eel_names
[ir
->coulombtype
]);
789 if (vsite
&& vsite
->numInterUpdategroupVsites
> 0)
793 fprintf(fplog
, "There are %d inter update-group virtual sites,\n"
794 "will an extra communication step for selected coordinates and forces\n",
795 vsite
->numInterUpdategroupVsites
);
797 init_domdec_vsites(dd
, vsite
->numInterUpdategroupVsites
);
800 if (dd
->comm
->systemInfo
.haveSplitConstraints
|| dd
->comm
->systemInfo
.haveSplitSettles
)
802 init_domdec_constraints(dd
, mtop
);
806 fprintf(fplog
, "\n");
810 /*! \brief Store a vsite interaction at the end of \p il
812 * This routine is very similar to add_ifunc, but vsites interactions
813 * have more work to do than other kinds of interactions, and the
814 * complex way nral (and thus vector contents) depends on ftype
815 * confuses static analysis tools unless we fuse the vsite
816 * atom-indexing organization code with the ifunc-adding code, so that
817 * they can see that nral is the same value. */
819 add_ifunc_for_vsites(t_iatom
*tiatoms
, const gmx_ga2la_t
&ga2la
,
820 int nral
, gmx_bool bHomeA
,
821 int a
, int a_gl
, int a_mol
,
822 const t_iatom
*iatoms
,
827 if (il
->nr
+1+nral
> il
->nalloc
)
829 il
->nalloc
= over_alloc_large(il
->nr
+1+nral
);
830 srenew(il
->iatoms
, il
->nalloc
);
832 liatoms
= il
->iatoms
+ il
->nr
;
836 tiatoms
[0] = iatoms
[0];
840 /* We know the local index of the first atom */
845 /* Convert later in make_local_vsites */
846 tiatoms
[1] = -a_gl
- 1;
849 for (int k
= 2; k
< 1+nral
; k
++)
851 int ak_gl
= a_gl
+ iatoms
[k
] - a_mol
;
852 if (const int *homeIndex
= ga2la
.findHome(ak_gl
))
854 tiatoms
[k
] = *homeIndex
;
858 /* Copy the global index, convert later in make_local_vsites */
859 tiatoms
[k
] = -(ak_gl
+ 1);
861 // Note that ga2la_get_home always sets the third parameter if
864 for (int k
= 0; k
< 1+nral
; k
++)
866 liatoms
[k
] = tiatoms
[k
];
870 /*! \brief Store a bonded interaction at the end of \p il */
871 static inline void add_ifunc(int nral
, const t_iatom
*tiatoms
, t_ilist
*il
)
876 if (il
->nr
+1+nral
> il
->nalloc
)
878 il
->nalloc
= over_alloc_large(il
->nr
+1+nral
);
879 srenew(il
->iatoms
, il
->nalloc
);
881 liatoms
= il
->iatoms
+ il
->nr
;
882 for (k
= 0; k
<= nral
; k
++)
884 liatoms
[k
] = tiatoms
[k
];
889 /*! \brief Store a position restraint in idef and iatoms, complex because the parameters are different for each entry */
890 static void add_posres(int mol
, int a_mol
, int numAtomsInMolecule
,
891 const gmx_molblock_t
*molb
,
892 t_iatom
*iatoms
, const t_iparams
*ip_in
,
898 /* This position restraint has not been added yet,
899 * so it's index is the current number of position restraints.
901 n
= idef
->il
[F_POSRES
].nr
/2;
902 if (n
+1 > idef
->iparams_posres_nalloc
)
904 idef
->iparams_posres_nalloc
= over_alloc_dd(n
+1);
905 srenew(idef
->iparams_posres
, idef
->iparams_posres_nalloc
);
907 ip
= &idef
->iparams_posres
[n
];
908 /* Copy the force constants */
909 *ip
= ip_in
[iatoms
[0]];
911 /* Get the position restraint coordinates from the molblock */
912 a_molb
= mol
*numAtomsInMolecule
+ a_mol
;
913 GMX_ASSERT(a_molb
< ssize(molb
->posres_xA
), "We need a sufficient number of position restraint coordinates");
914 ip
->posres
.pos0A
[XX
] = molb
->posres_xA
[a_molb
][XX
];
915 ip
->posres
.pos0A
[YY
] = molb
->posres_xA
[a_molb
][YY
];
916 ip
->posres
.pos0A
[ZZ
] = molb
->posres_xA
[a_molb
][ZZ
];
917 if (!molb
->posres_xB
.empty())
919 ip
->posres
.pos0B
[XX
] = molb
->posres_xB
[a_molb
][XX
];
920 ip
->posres
.pos0B
[YY
] = molb
->posres_xB
[a_molb
][YY
];
921 ip
->posres
.pos0B
[ZZ
] = molb
->posres_xB
[a_molb
][ZZ
];
925 ip
->posres
.pos0B
[XX
] = ip
->posres
.pos0A
[XX
];
926 ip
->posres
.pos0B
[YY
] = ip
->posres
.pos0A
[YY
];
927 ip
->posres
.pos0B
[ZZ
] = ip
->posres
.pos0A
[ZZ
];
929 /* Set the parameter index for idef->iparams_posre */
933 /*! \brief Store a flat-bottomed position restraint in idef and iatoms, complex because the parameters are different for each entry */
934 static void add_fbposres(int mol
, int a_mol
, int numAtomsInMolecule
,
935 const gmx_molblock_t
*molb
,
936 t_iatom
*iatoms
, const t_iparams
*ip_in
,
942 /* This flat-bottom position restraint has not been added yet,
943 * so it's index is the current number of position restraints.
945 n
= idef
->il
[F_FBPOSRES
].nr
/2;
946 if (n
+1 > idef
->iparams_fbposres_nalloc
)
948 idef
->iparams_fbposres_nalloc
= over_alloc_dd(n
+1);
949 srenew(idef
->iparams_fbposres
, idef
->iparams_fbposres_nalloc
);
951 ip
= &idef
->iparams_fbposres
[n
];
952 /* Copy the force constants */
953 *ip
= ip_in
[iatoms
[0]];
955 /* Get the position restraint coordinats from the molblock */
956 a_molb
= mol
*numAtomsInMolecule
+ a_mol
;
957 GMX_ASSERT(a_molb
< ssize(molb
->posres_xA
), "We need a sufficient number of position restraint coordinates");
958 /* Take reference positions from A position of normal posres */
959 ip
->fbposres
.pos0
[XX
] = molb
->posres_xA
[a_molb
][XX
];
960 ip
->fbposres
.pos0
[YY
] = molb
->posres_xA
[a_molb
][YY
];
961 ip
->fbposres
.pos0
[ZZ
] = molb
->posres_xA
[a_molb
][ZZ
];
963 /* Note: no B-type for flat-bottom posres */
965 /* Set the parameter index for idef->iparams_posre */
969 /*! \brief Store a virtual site interaction, complex because of PBC and recursion */
970 static void add_vsite(const gmx_ga2la_t
&ga2la
,
971 gmx::ArrayRef
<const int> index
,
972 gmx::ArrayRef
<const int> rtil
,
974 gmx_bool bHomeA
, int a
, int a_gl
, int a_mol
,
975 const t_iatom
*iatoms
,
979 t_iatom tiatoms
[1+MAXATOMLIST
];
980 int j
, ftype_r
, nral_r
;
982 /* Add this interaction to the local topology */
983 add_ifunc_for_vsites(tiatoms
, ga2la
, nral
, bHomeA
, a
, a_gl
, a_mol
, iatoms
, &idef
->il
[ftype
]);
987 /* Check for recursion */
988 for (k
= 2; k
< 1+nral
; k
++)
990 if ((iatoms
[1+nral
] & (2<<k
)) && (tiatoms
[k
] < 0))
992 /* This construction atoms is a vsite and not a home atom */
995 fprintf(debug
, "Constructing atom %d of vsite atom %d is a vsite and non-home\n", iatoms
[k
]+1, a_mol
+1);
997 /* Find the vsite construction */
999 /* Check all interactions assigned to this atom */
1000 j
= index
[iatoms
[k
]];
1001 while (j
< index
[iatoms
[k
]+1])
1003 ftype_r
= rtil
[j
++];
1004 nral_r
= NRAL(ftype_r
);
1005 if (interaction_function
[ftype_r
].flags
& IF_VSITE
)
1007 /* Add this vsite (recursion) */
1008 add_vsite(ga2la
, index
, rtil
, ftype_r
, nral_r
,
1009 FALSE
, -1, a_gl
+iatoms
[k
]-iatoms
[1], iatoms
[k
],
1013 j
+= 1 + nral_rt(ftype_r
);
1020 /*! \brief Returns the squared distance between atoms \p i and \p j */
1021 static real
dd_dist2(t_pbc
*pbc_null
, const rvec
*x
, const int i
, int j
)
1027 pbc_dx_aiuc(pbc_null
, x
[i
], x
[j
], dx
);
1031 rvec_sub(x
[i
], x
[j
], dx
);
1037 /*! \brief Append t_blocka block structures 1 to nsrc in src to *dest */
1038 static void combine_blocka(t_blocka
*dest
,
1039 gmx::ArrayRef
<const thread_work_t
> src
)
1041 int ni
= src
.back().excl
.nr
;
1043 for (const thread_work_t
&th_work
: src
)
1045 na
+= th_work
.excl
.nra
;
1047 if (ni
+ 1 > dest
->nalloc_index
)
1049 dest
->nalloc_index
= over_alloc_large(ni
+1);
1050 srenew(dest
->index
, dest
->nalloc_index
);
1052 if (dest
->nra
+ na
> dest
->nalloc_a
)
1054 dest
->nalloc_a
= over_alloc_large(dest
->nra
+na
);
1055 srenew(dest
->a
, dest
->nalloc_a
);
1057 for (gmx::index s
= 1; s
< src
.ssize(); s
++)
1059 for (int i
= dest
->nr
+ 1; i
< src
[s
].excl
.nr
+ 1; i
++)
1061 dest
->index
[i
] = dest
->nra
+ src
[s
].excl
.index
[i
];
1063 for (int i
= 0; i
< src
[s
].excl
.nra
; i
++)
1065 dest
->a
[dest
->nra
+i
] = src
[s
].excl
.a
[i
];
1067 dest
->nr
= src
[s
].excl
.nr
;
1068 dest
->nra
+= src
[s
].excl
.nra
;
1072 /*! \brief Append t_idef structures 1 to nsrc in src to *dest */
1073 static void combine_idef(t_idef
*dest
,
1074 gmx::ArrayRef
<const thread_work_t
> src
)
1078 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
1081 for (gmx::index s
= 1; s
< src
.ssize(); s
++)
1083 n
+= src
[s
].idef
.il
[ftype
].nr
;
1089 ild
= &dest
->il
[ftype
];
1091 if (ild
->nr
+ n
> ild
->nalloc
)
1093 ild
->nalloc
= over_alloc_large(ild
->nr
+n
);
1094 srenew(ild
->iatoms
, ild
->nalloc
);
1097 for (gmx::index s
= 1; s
< src
.ssize(); s
++)
1099 const t_ilist
&ils
= src
[s
].idef
.il
[ftype
];
1101 for (int i
= 0; i
< ils
.nr
; i
++)
1103 ild
->iatoms
[ild
->nr
+ i
] = ils
.iatoms
[i
];
1109 /* Position restraints need an additional treatment */
1110 if (ftype
== F_POSRES
|| ftype
== F_FBPOSRES
)
1112 int nposres
= dest
->il
[ftype
].nr
/2;
1113 // TODO: Simplify this code using std::vector
1114 t_iparams
* &iparams_dest
= (ftype
== F_POSRES
? dest
->iparams_posres
: dest
->iparams_fbposres
);
1115 int &posres_nalloc
= (ftype
== F_POSRES
? dest
->iparams_posres_nalloc
: dest
->iparams_fbposres_nalloc
);
1116 if (nposres
> posres_nalloc
)
1118 posres_nalloc
= over_alloc_large(nposres
);
1119 srenew(iparams_dest
, posres_nalloc
);
1122 /* Set nposres to the number of original position restraints in dest */
1123 for (gmx::index s
= 1; s
< src
.ssize(); s
++)
1125 nposres
-= src
[s
].idef
.il
[ftype
].nr
/2;
1128 for (gmx::index s
= 1; s
< src
.ssize(); s
++)
1130 const t_iparams
*iparams_src
= (ftype
== F_POSRES
? src
[s
].idef
.iparams_posres
: src
[s
].idef
.iparams_fbposres
);
1132 for (int i
= 0; i
< src
[s
].idef
.il
[ftype
].nr
/2; i
++)
1134 /* Correct the index into iparams_posres */
1135 dest
->il
[ftype
].iatoms
[nposres
*2] = nposres
;
1136 /* Copy the position restraint force parameters */
1137 iparams_dest
[nposres
] = iparams_src
[i
];
1146 /*! \brief Check and when available assign bonded interactions for local atom i
1149 check_assign_interactions_atom(int i
, int i_gl
,
1151 int numAtomsInMolecule
,
1152 gmx::ArrayRef
<const int> index
,
1153 gmx::ArrayRef
<const int> rtil
,
1154 gmx_bool bInterMolInteractions
,
1155 int ind_start
, int ind_end
,
1156 const gmx_domdec_t
*dd
,
1157 const gmx_domdec_zones_t
*zones
,
1158 const gmx_molblock_t
*molb
,
1159 gmx_bool bRCheckMB
, const ivec rcheck
, gmx_bool bRCheck2B
,
1163 const t_iparams
*ip_in
,
1174 t_iatom tiatoms
[1 + MAXATOMLIST
];
1176 const int ftype
= rtil
[j
++];
1177 auto iatoms
= gmx::constArrayRefFromArray(rtil
.data() + j
, rtil
.size() - j
);
1178 const int nral
= NRAL(ftype
);
1179 if (interaction_function
[ftype
].flags
& IF_VSITE
)
1181 assert(!bInterMolInteractions
);
1182 /* The vsite construction goes where the vsite itself is */
1185 add_vsite(*dd
->ga2la
, index
, rtil
, ftype
, nral
,
1186 TRUE
, i
, i_gl
, i_mol
,
1187 iatoms
.data(), idef
);
1196 tiatoms
[0] = iatoms
[0];
1200 assert(!bInterMolInteractions
);
1201 /* Assign single-body interactions to the home zone */
1206 if (ftype
== F_POSRES
)
1208 add_posres(mol
, i_mol
, numAtomsInMolecule
,
1209 molb
, tiatoms
, ip_in
, idef
);
1211 else if (ftype
== F_FBPOSRES
)
1213 add_fbposres(mol
, i_mol
, numAtomsInMolecule
,
1214 molb
, tiatoms
, ip_in
, idef
);
1224 /* This is a two-body interaction, we can assign
1225 * analogous to the non-bonded assignments.
1229 if (!bInterMolInteractions
)
1231 /* Get the global index using the offset in the molecule */
1232 k_gl
= i_gl
+ iatoms
[2] - i_mol
;
1238 if (const auto *entry
= dd
->ga2la
->find(k_gl
))
1240 int kz
= entry
->cell
;
1245 /* Check zone interaction assignments */
1246 bUse
= ((iz
< zones
->nizone
&&
1248 kz
>= zones
->izone
[iz
].j0
&&
1249 kz
< zones
->izone
[iz
].j1
) ||
1250 (kz
< zones
->nizone
&&
1252 iz
>= zones
->izone
[kz
].j0
&&
1253 iz
< zones
->izone
[kz
].j1
));
1256 GMX_ASSERT(ftype
!= F_CONSTR
|| (iz
== 0 && kz
== 0),
1257 "Constraint assigned here should only involve home atoms");
1260 tiatoms
[2] = entry
->la
;
1261 /* If necessary check the cgcm distance */
1263 dd_dist2(pbc_null
, cg_cm
,
1264 tiatoms
[1], tiatoms
[2]) >= rc2
)
1277 /* Assign this multi-body bonded interaction to
1278 * the local node if we have all the atoms involved
1279 * (local or communicated) and the minimum zone shift
1280 * in each dimension is zero, for dimensions
1281 * with 2 DD cells an extra check may be necessary.
1283 ivec k_zero
, k_plus
;
1289 for (k
= 1; k
<= nral
&& bUse
; k
++)
1292 if (!bInterMolInteractions
)
1294 /* Get the global index using the offset in the molecule */
1295 k_gl
= i_gl
+ iatoms
[k
] - i_mol
;
1301 const auto *entry
= dd
->ga2la
->find(k_gl
);
1302 if (entry
== nullptr || entry
->cell
>= zones
->n
)
1304 /* We do not have this atom of this interaction
1305 * locally, or it comes from more than one cell
1314 tiatoms
[k
] = entry
->la
;
1315 for (d
= 0; d
< DIM
; d
++)
1317 if (zones
->shift
[entry
->cell
][d
] == 0)
1329 (k_zero
[XX
] != 0) && (k_zero
[YY
] != 0) && (k_zero
[ZZ
] != 0));
1334 for (d
= 0; (d
< DIM
&& bUse
); d
++)
1336 /* Check if the cg_cm distance falls within
1337 * the cut-off to avoid possible multiple
1338 * assignments of bonded interactions.
1342 dd_dist2(pbc_null
, cg_cm
,
1343 tiatoms
[k_zero
[d
]], tiatoms
[k_plus
[d
]]) >= rc2
)
1352 /* Add this interaction to the local topology */
1353 add_ifunc(nral
, tiatoms
, &idef
->il
[ftype
]);
1354 /* Sum so we can check in global_stat
1355 * if we have everything.
1358 !(interaction_function
[ftype
].flags
& IF_LIMZERO
))
1368 /*! \brief This function looks up and assigns bonded interactions for zone iz.
1370 * With thread parallelizing each thread acts on a different atom range:
1371 * at_start to at_end.
1373 static int make_bondeds_zone(gmx_domdec_t
*dd
,
1374 const gmx_domdec_zones_t
*zones
,
1375 const std::vector
<gmx_molblock_t
> &molb
,
1376 gmx_bool bRCheckMB
, ivec rcheck
, gmx_bool bRCheck2B
,
1378 t_pbc
*pbc_null
, rvec
*cg_cm
,
1379 const t_iparams
*ip_in
,
1382 gmx::RangePartitioning::Block atomRange
)
1384 int mb
, mt
, mol
, i_mol
;
1386 gmx_reverse_top_t
*rt
;
1389 rt
= dd
->reverse_top
;
1391 bBCheck
= rt
->bBCheck
;
1395 for (int i
: atomRange
)
1397 /* Get the global atom number */
1398 const int i_gl
= dd
->globalAtomIndices
[i
];
1399 global_atomnr_to_moltype_ind(rt
, i_gl
, &mb
, &mt
, &mol
, &i_mol
);
1400 /* Check all intramolecular interactions assigned to this atom */
1401 gmx::ArrayRef
<const int> index
= rt
->ril_mt
[mt
].index
;
1402 gmx::ArrayRef
<const t_iatom
> rtil
= rt
->ril_mt
[mt
].il
;
1404 check_assign_interactions_atom(i
, i_gl
, mol
, i_mol
,
1405 rt
->ril_mt
[mt
].numAtomsInMolecule
,
1407 index
[i_mol
], index
[i_mol
+1],
1410 bRCheckMB
, rcheck
, bRCheck2B
, rc2
,
1420 if (rt
->bIntermolecularInteractions
)
1422 /* Check all intermolecular interactions assigned to this atom */
1423 index
= rt
->ril_intermol
.index
;
1424 rtil
= rt
->ril_intermol
.il
;
1426 check_assign_interactions_atom(i
, i_gl
, mol
, i_mol
,
1427 rt
->ril_mt
[mt
].numAtomsInMolecule
,
1429 index
[i_gl
], index
[i_gl
+ 1],
1432 bRCheckMB
, rcheck
, bRCheck2B
, rc2
,
1443 return nbonded_local
;
1446 /*! \brief Set the exclusion data for i-zone \p iz for the case of no exclusions */
1447 static void set_no_exclusions_zone(const gmx_domdec_zones_t
*zones
,
1451 for (int a
= zones
->cg_range
[iz
]; a
< zones
->cg_range
[iz
+ 1]; a
++)
1453 lexcls
->index
[a
+ 1] = lexcls
->nra
;
1457 /*! \brief Set the exclusion data for i-zone \p iz
1459 * This is a legacy version for the group scheme of the same routine below.
1460 * Here charge groups and distance checks to ensure unique exclusions
1463 static int make_exclusions_zone_cg(gmx_domdec_t
*dd
, gmx_domdec_zones_t
*zones
,
1464 const std::vector
<gmx_moltype_t
> &moltype
,
1465 gmx_bool bRCheck
, real rc2
,
1466 t_pbc
*pbc_null
, rvec
*cg_cm
,
1470 int cg_start
, int cg_end
)
1474 const t_blocka
*excls
;
1476 const gmx_ga2la_t
&ga2la
= *dd
->ga2la
;
1478 // TODO: Replace this by a more standard range
1479 const gmx::RangePartitioning::Block
jRange(zones
->izone
[iz
].jcg0
,
1480 zones
->izone
[iz
].jcg1
);
1482 n_excl_at_max
= dd
->reverse_top
->n_excl_at_max
;
1484 /* We set the end index, but note that we might not start at zero here */
1485 lexcls
->nr
= cg_end
;
1487 int n
= lexcls
->nra
;
1489 for (int la
= cg_start
; la
< cg_end
; la
++)
1491 if (n
+ (cg_end
- cg_start
)*n_excl_at_max
> lexcls
->nalloc_a
)
1493 lexcls
->nalloc_a
= over_alloc_large(n
+ (cg_end
- cg_start
)*n_excl_at_max
);
1494 srenew(lexcls
->a
, lexcls
->nalloc_a
);
1496 if (GET_CGINFO_EXCL_INTER(cginfo
[la
]) ||
1497 !GET_CGINFO_EXCL_INTRA(cginfo
[la
]))
1499 /* Copy the exclusions from the global top */
1500 lexcls
->index
[la
] = n
;
1501 int a_gl
= dd
->globalAtomIndices
[la
];
1503 global_atomnr_to_moltype_ind(dd
->reverse_top
, a_gl
, &mb
, &mt
, &mol
, &a_mol
);
1504 excls
= &moltype
[mt
].excls
;
1505 for (int j
= excls
->index
[a_mol
]; j
< excls
->index
[a_mol
+1]; j
++)
1507 int aj_mol
= excls
->a
[j
];
1508 /* Since exclusions are pair interactions,
1509 * just like non-bonded interactions,
1510 * they can be assigned properly up
1511 * to the DD cutoff (not cutoff_min as
1512 * for the other bonded interactions).
1514 if (const auto *jEntry
= ga2la
.find(a_gl
+ aj_mol
- a_mol
))
1516 if (iz
== 0 && jEntry
->cell
== 0)
1518 lexcls
->a
[n
++] = jEntry
->la
;
1519 /* Check to avoid double counts */
1520 if (jEntry
->la
> la
)
1525 else if (jRange
.inRange(jEntry
->la
) &&
1527 dd_dist2(pbc_null
, cg_cm
, la
, jEntry
->la
) < rc2
))
1529 /* jla > la, since jRange.begin() > la */
1530 lexcls
->a
[n
++] = jEntry
->la
;
1538 /* There are no inter-atomic excls and this atom is self-excluded.
1539 * These exclusions are only required for zone 0,
1540 * since other zones do not see themselves.
1544 lexcls
->index
[la
] = n
;
1545 lexcls
->a
[n
++] = la
;
1549 lexcls
->index
[la
] = n
;
1554 lexcls
->index
[lexcls
->nr
] = n
;
1560 /*! \brief Set the exclusion data for i-zone \p iz */
1561 static void make_exclusions_zone(gmx_domdec_t
*dd
, gmx_domdec_zones_t
*zones
,
1562 const std::vector
<gmx_moltype_t
> &moltype
,
1563 const int *cginfo
, t_blocka
*lexcls
, int iz
,
1564 int at_start
, int at_end
,
1565 const gmx::ArrayRef
<const int> intermolecularExclusionGroup
)
1567 int n_excl_at_max
, n
, at
;
1569 const gmx_ga2la_t
&ga2la
= *dd
->ga2la
;
1571 // TODO: Replace this by a more standard range
1572 const gmx::RangePartitioning::Block
jRange(zones
->izone
[iz
].jcg0
,
1573 zones
->izone
[iz
].jcg1
);
1575 n_excl_at_max
= dd
->reverse_top
->n_excl_at_max
;
1577 /* We set the end index, but note that we might not start at zero here */
1578 lexcls
->nr
= at_end
;
1581 for (at
= at_start
; at
< at_end
; at
++)
1583 if (n
+ 1000 > lexcls
->nalloc_a
)
1585 lexcls
->nalloc_a
= over_alloc_large(n
+ 1000);
1586 srenew(lexcls
->a
, lexcls
->nalloc_a
);
1589 if (GET_CGINFO_EXCL_INTER(cginfo
[at
]))
1591 int a_gl
, mb
, mt
, mol
, a_mol
, j
;
1592 const t_blocka
*excls
;
1594 if (n
+ n_excl_at_max
> lexcls
->nalloc_a
)
1596 lexcls
->nalloc_a
= over_alloc_large(n
+ n_excl_at_max
);
1597 srenew(lexcls
->a
, lexcls
->nalloc_a
);
1600 /* Copy the exclusions from the global top */
1601 lexcls
->index
[at
] = n
;
1602 a_gl
= dd
->globalAtomIndices
[at
];
1603 global_atomnr_to_moltype_ind(dd
->reverse_top
, a_gl
,
1604 &mb
, &mt
, &mol
, &a_mol
);
1605 excls
= &moltype
[mt
].excls
;
1606 for (j
= excls
->index
[a_mol
]; j
< excls
->index
[a_mol
+ 1]; j
++)
1608 const int aj_mol
= excls
->a
[j
];
1610 if (const auto *jEntry
= ga2la
.find(a_gl
+ aj_mol
- a_mol
))
1612 /* This check is not necessary, but it can reduce
1613 * the number of exclusions in the list, which in turn
1614 * can speed up the pair list construction a bit.
1616 if (jRange
.inRange(jEntry
->la
))
1618 lexcls
->a
[n
++] = jEntry
->la
;
1625 /* We don't need exclusions for this atom */
1626 lexcls
->index
[at
] = n
;
1629 bool isExcludedAtom
= !intermolecularExclusionGroup
.empty() &&
1630 std::find(intermolecularExclusionGroup
.begin(),
1631 intermolecularExclusionGroup
.end(),
1632 dd
->globalAtomIndices
[at
]) !=
1633 intermolecularExclusionGroup
.end();
1637 if (n
+ intermolecularExclusionGroup
.ssize() > lexcls
->nalloc_a
)
1640 over_alloc_large(n
+ intermolecularExclusionGroup
.size());
1641 srenew(lexcls
->a
, lexcls
->nalloc_a
);
1643 for (int qmAtomGlobalIndex
: intermolecularExclusionGroup
)
1645 if (const auto *entry
= dd
->ga2la
->find(qmAtomGlobalIndex
))
1647 lexcls
->a
[n
++] = entry
->la
;
1653 lexcls
->index
[lexcls
->nr
] = n
;
1658 /*! \brief Ensure we have enough space in \p ba for \p nindex_max indices */
1659 static void check_alloc_index(t_blocka
*ba
, int nindex_max
)
1661 if (nindex_max
+1 > ba
->nalloc_index
)
1663 ba
->nalloc_index
= over_alloc_dd(nindex_max
+1);
1664 srenew(ba
->index
, ba
->nalloc_index
);
1668 /*! \brief Ensure that we have enough space for exclusion storate in \p lexcls */
1669 static void check_exclusions_alloc(gmx_domdec_t
*dd
, gmx_domdec_zones_t
*zones
,
1672 const int nr
= zones
->izone
[zones
->nizone
- 1].cg1
;
1674 check_alloc_index(lexcls
, nr
);
1676 for (size_t thread
= 1; thread
< dd
->reverse_top
->th_work
.size(); thread
++)
1678 check_alloc_index(&dd
->reverse_top
->th_work
[thread
].excl
, nr
);
1682 /*! \brief Set the total count indexes for the local exclusions, needed by several functions */
1683 static void finish_local_exclusions(gmx_domdec_t
*dd
, gmx_domdec_zones_t
*zones
,
1686 // TODO: Replace this by a more standard range
1687 const gmx::RangePartitioning::Block
nonhomeIzonesAtomRange(zones
->izone
[0].cg1
,
1688 zones
->izone
[zones
->nizone
- 1].cg1
);
1690 if (dd
->n_intercg_excl
== 0)
1692 /* There are no exclusions involving non-home charge groups,
1693 * but we need to set the indices for neighborsearching.
1695 for (int la
: nonhomeIzonesAtomRange
)
1697 lexcls
->index
[la
] = lexcls
->nra
;
1700 /* nr is only used to loop over the exclusions for Ewald and RF,
1701 * so we can set it to the number of home atoms for efficiency.
1703 lexcls
->nr
= nonhomeIzonesAtomRange
.begin();
1707 lexcls
->nr
= nonhomeIzonesAtomRange
.end();
1711 /*! \brief Clear a t_idef struct */
1712 static void clear_idef(t_idef
*idef
)
1716 /* Clear the counts */
1717 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
1719 idef
->il
[ftype
].nr
= 0;
1723 /*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
1724 static int make_local_bondeds_excls(gmx_domdec_t
*dd
,
1725 gmx_domdec_zones_t
*zones
,
1726 const gmx_mtop_t
*mtop
,
1728 gmx_bool bRCheckMB
, ivec rcheck
, gmx_bool bRCheck2B
,
1730 t_pbc
*pbc_null
, rvec
*cg_cm
,
1732 t_blocka
*lexcls
, int *excl_count
)
1734 int nzone_bondeds
, nzone_excl
;
1735 int izone
, cg0
, cg1
;
1738 gmx_reverse_top_t
*rt
;
1740 if (dd
->reverse_top
->bInterCGInteractions
)
1742 nzone_bondeds
= zones
->n
;
1746 /* Only single charge group (or atom) molecules, so interactions don't
1747 * cross zone boundaries and we only need to assign in the home zone.
1752 if (dd
->n_intercg_excl
> 0)
1754 /* We only use exclusions from i-zones to i- and j-zones */
1755 nzone_excl
= zones
->nizone
;
1759 /* There are no inter-cg exclusions and only zone 0 sees itself */
1763 check_exclusions_alloc(dd
, zones
, lexcls
);
1765 rt
= dd
->reverse_top
;
1769 /* Clear the counts */
1777 for (izone
= 0; izone
< nzone_bondeds
; izone
++)
1779 cg0
= zones
->cg_range
[izone
];
1780 cg1
= zones
->cg_range
[izone
+ 1];
1782 const int numThreads
= rt
->th_work
.size();
1783 #pragma omp parallel for num_threads(numThreads) schedule(static)
1784 for (int thread
= 0; thread
< numThreads
; thread
++)
1792 cg0t
= cg0
+ ((cg1
- cg0
)* thread
)/numThreads
;
1793 cg1t
= cg0
+ ((cg1
- cg0
)*(thread
+1))/numThreads
;
1801 idef_t
= &rt
->th_work
[thread
].idef
;
1805 rt
->th_work
[thread
].nbonded
=
1806 make_bondeds_zone(dd
, zones
,
1808 bRCheckMB
, rcheck
, bRCheck2B
, rc2
,
1809 pbc_null
, cg_cm
, idef
->iparams
,
1812 gmx::RangePartitioning::Block(cg0t
, cg1t
));
1814 if (izone
< nzone_excl
)
1822 excl_t
= &rt
->th_work
[thread
].excl
;
1827 if (!rt
->bExclRequired
)
1829 /* No charge groups and no distance check required */
1830 make_exclusions_zone(dd
, zones
, mtop
->moltype
, cginfo
,
1831 excl_t
, izone
, cg0t
,
1833 mtop
->intermolecularExclusionGroup
);
1837 rt
->th_work
[thread
].excl_count
=
1838 make_exclusions_zone_cg(dd
, zones
,
1839 mtop
->moltype
, bRCheck2B
, rc2
,
1840 pbc_null
, cg_cm
, cginfo
,
1847 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
1850 if (rt
->th_work
.size() > 1)
1852 combine_idef(idef
, rt
->th_work
);
1855 for (const thread_work_t
&th_work
: rt
->th_work
)
1857 nbonded_local
+= th_work
.nbonded
;
1860 if (izone
< nzone_excl
)
1862 if (rt
->th_work
.size() > 1)
1864 combine_blocka(lexcls
, rt
->th_work
);
1867 for (const thread_work_t
&th_work
: rt
->th_work
)
1869 *excl_count
+= th_work
.excl_count
;
1874 /* Some zones might not have exclusions, but some code still needs to
1875 * loop over the index, so we set the indices here.
1877 for (izone
= nzone_excl
; izone
< zones
->nizone
; izone
++)
1879 set_no_exclusions_zone(zones
, izone
, lexcls
);
1882 finish_local_exclusions(dd
, zones
, lexcls
);
1885 fprintf(debug
, "We have %d exclusions, check count %d\n",
1886 lexcls
->nra
, *excl_count
);
1889 return nbonded_local
;
1892 void dd_make_local_top(gmx_domdec_t
*dd
, gmx_domdec_zones_t
*zones
,
1893 int npbcdim
, matrix box
,
1894 rvec cellsize_min
, const ivec npulse
,
1897 const gmx_mtop_t
&mtop
, gmx_localtop_t
*ltop
)
1899 gmx_bool bRCheckMB
, bRCheck2B
;
1903 t_pbc pbc
, *pbc_null
= nullptr;
1907 fprintf(debug
, "Making local topology\n");
1913 if (dd
->reverse_top
->bInterCGInteractions
)
1915 /* We need to check to which cell bondeds should be assigned */
1916 rc
= dd_cutoff_twobody(dd
);
1919 fprintf(debug
, "Two-body bonded cut-off distance is %g\n", rc
);
1922 /* Should we check cg_cm distances when assigning bonded interactions? */
1923 for (d
= 0; d
< DIM
; d
++)
1926 /* Only need to check for dimensions where the part of the box
1927 * that is not communicated is smaller than the cut-off.
1929 if (d
< npbcdim
&& dd
->nc
[d
] > 1 &&
1930 (dd
->nc
[d
] - npulse
[d
])*cellsize_min
[d
] < 2*rc
)
1937 /* Check for interactions between two atoms,
1938 * where we can allow interactions up to the cut-off,
1939 * instead of up to the smallest cell dimension.
1946 "dim %d cellmin %f bonded rcheck[%d] = %d, bRCheck2B = %s\n",
1947 d
, cellsize_min
[d
], d
, rcheck
[d
], gmx::boolToString(bRCheck2B
));
1950 if (bRCheckMB
|| bRCheck2B
)
1954 pbc_null
= set_pbc_dd(&pbc
, fr
->ePBC
, dd
->nc
, TRUE
, box
);
1964 make_local_bondeds_excls(dd
, zones
, &mtop
, fr
->cginfo
.data(),
1965 bRCheckMB
, rcheck
, bRCheck2B
, rc
,
1966 pbc_null
, cgcm_or_x
,
1968 <op
->excls
, &nexcl
);
1970 /* The ilist is not sorted yet,
1971 * we can only do this when we have the charge arrays.
1973 ltop
->idef
.ilsort
= ilsortUNKNOWN
;
1975 if (dd
->reverse_top
->bExclRequired
)
1977 dd
->nbonded_local
+= nexcl
;
1980 ltop
->atomtypes
= mtop
.atomtypes
;
1983 void dd_sort_local_top(gmx_domdec_t
*dd
, const t_mdatoms
*mdatoms
,
1984 gmx_localtop_t
*ltop
)
1986 if (dd
->reverse_top
->ilsort
== ilsortNO_FE
)
1988 ltop
->idef
.ilsort
= ilsortNO_FE
;
1992 gmx_sort_ilist_fe(<op
->idef
, mdatoms
->chargeA
, mdatoms
->chargeB
);
1996 void dd_init_local_top(const gmx_mtop_t
&top_global
,
1997 gmx_localtop_t
*top
)
1999 /* TODO: Get rid of the const casts below, e.g. by using a reference */
2000 top
->idef
.ntypes
= top_global
.ffparams
.numTypes();
2001 top
->idef
.atnr
= top_global
.ffparams
.atnr
;
2002 top
->idef
.functype
= const_cast<t_functype
*>(top_global
.ffparams
.functype
.data());
2003 top
->idef
.iparams
= const_cast<t_iparams
*>(top_global
.ffparams
.iparams
.data());
2004 top
->idef
.fudgeQQ
= top_global
.ffparams
.fudgeQQ
;
2005 top
->idef
.cmap_grid
= new gmx_cmap_t
;
2006 *top
->idef
.cmap_grid
= top_global
.ffparams
.cmap_grid
;
2008 top
->idef
.ilsort
= ilsortUNKNOWN
;
2009 top
->useInDomainDecomp_
= true;
2012 void dd_init_local_state(gmx_domdec_t
*dd
,
2013 const t_state
*state_global
, t_state
*state_local
)
2015 int buf
[NITEM_DD_INIT_LOCAL_STATE
];
2019 buf
[0] = state_global
->flags
;
2020 buf
[1] = state_global
->ngtc
;
2021 buf
[2] = state_global
->nnhpres
;
2022 buf
[3] = state_global
->nhchainlength
;
2023 buf
[4] = state_global
->dfhist
? state_global
->dfhist
->nlambda
: 0;
2025 dd_bcast(dd
, NITEM_DD_INIT_LOCAL_STATE
*sizeof(int), buf
);
2027 init_gtc_state(state_local
, buf
[1], buf
[2], buf
[3]);
2028 init_dfhist_state(state_local
, buf
[4]);
2029 state_local
->flags
= buf
[0];
2032 /*! \brief Check if a link is stored in \p link between charge groups \p cg_gl and \p cg_gl_j and if not so, store a link */
2033 static void check_link(t_blocka
*link
, int cg_gl
, int cg_gl_j
)
2039 for (k
= link
->index
[cg_gl
]; k
< link
->index
[cg_gl
+1]; k
++)
2041 GMX_RELEASE_ASSERT(link
->a
, "Inconsistent NULL pointer while making charge-group links");
2042 if (link
->a
[k
] == cg_gl_j
)
2049 GMX_RELEASE_ASSERT(link
->a
|| link
->index
[cg_gl
+1]+1 > link
->nalloc_a
,
2050 "Inconsistent allocation of link");
2051 /* Add this charge group link */
2052 if (link
->index
[cg_gl
+1]+1 > link
->nalloc_a
)
2054 link
->nalloc_a
= over_alloc_large(link
->index
[cg_gl
+1]+1);
2055 srenew(link
->a
, link
->nalloc_a
);
2057 link
->a
[link
->index
[cg_gl
+1]] = cg_gl_j
;
2058 link
->index
[cg_gl
+1]++;
2062 /*! \brief Return a vector of the charge group index for all atoms */
2063 static std::vector
<int> make_at2cg(const t_block
&cgs
)
2065 std::vector
<int> at2cg(cgs
.index
[cgs
.nr
]);
2066 for (int cg
= 0; cg
< cgs
.nr
; cg
++)
2068 for (int a
= cgs
.index
[cg
]; a
< cgs
.index
[cg
+ 1]; a
++)
2077 t_blocka
*make_charge_group_links(const gmx_mtop_t
*mtop
, gmx_domdec_t
*dd
,
2078 cginfo_mb_t
*cginfo_mb
)
2080 gmx_bool bExclRequired
;
2082 cginfo_mb_t
*cgi_mb
;
2084 /* For each charge group make a list of other charge groups
2085 * in the system that a linked to it via bonded interactions
2086 * which are also stored in reverse_top.
2089 bExclRequired
= dd
->reverse_top
->bExclRequired
;
2091 reverse_ilist_t ril_intermol
;
2092 if (mtop
->bIntermolecularInteractions
)
2094 if (ncg_mtop(mtop
) < mtop
->natoms
)
2096 gmx_fatal(FARGS
, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
2101 atoms
.nr
= mtop
->natoms
;
2102 atoms
.atom
= nullptr;
2104 GMX_RELEASE_ASSERT(mtop
->intermolecular_ilist
, "We should have an ilist when intermolecular interactions are on");
2106 make_reverse_ilist(*mtop
->intermolecular_ilist
,
2108 FALSE
, FALSE
, FALSE
, TRUE
, &ril_intermol
);
2112 snew(link
->index
, ncg_mtop(mtop
)+1);
2119 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
2121 const gmx_molblock_t
&molb
= mtop
->molblock
[mb
];
2126 const gmx_moltype_t
&molt
= mtop
->moltype
[molb
.type
];
2127 const t_block
&cgs
= molt
.cgs
;
2128 const t_blocka
&excls
= molt
.excls
;
2129 std::vector
<int> a2c
= make_at2cg(cgs
);
2130 /* Make a reverse ilist in which the interactions are linked
2131 * to all atoms, not only the first atom as in gmx_reverse_top.
2132 * The constraints are discarded here.
2134 reverse_ilist_t ril
;
2135 make_reverse_ilist(molt
.ilist
, &molt
.atoms
,
2136 FALSE
, FALSE
, FALSE
, TRUE
, &ril
);
2138 cgi_mb
= &cginfo_mb
[mb
];
2141 for (mol
= 0; mol
< (mtop
->bIntermolecularInteractions
? molb
.nmol
: 1); mol
++)
2143 for (int cg
= 0; cg
< cgs
.nr
; cg
++)
2145 int cg_gl
= cg_offset
+ cg
;
2146 link
->index
[cg_gl
+1] = link
->index
[cg_gl
];
2147 for (int a
= cgs
.index
[cg
]; a
< cgs
.index
[cg
+ 1]; a
++)
2149 int i
= ril
.index
[a
];
2150 while (i
< ril
.index
[a
+1])
2152 int ftype
= ril
.il
[i
++];
2153 int nral
= NRAL(ftype
);
2154 /* Skip the ifunc index */
2156 for (int j
= 0; j
< nral
; j
++)
2158 int aj
= ril
.il
[i
+ j
];
2161 check_link(link
, cg_gl
, cg_offset
+a2c
[aj
]);
2164 i
+= nral_rt(ftype
);
2168 /* Exclusions always go both ways */
2169 for (int j
= excls
.index
[a
]; j
< excls
.index
[a
+ 1]; j
++)
2171 int aj
= excls
.a
[j
];
2174 check_link(link
, cg_gl
, cg_offset
+a2c
[aj
]);
2179 if (mtop
->bIntermolecularInteractions
)
2181 int i
= ril_intermol
.index
[a
];
2182 while (i
< ril_intermol
.index
[a
+1])
2184 int ftype
= ril_intermol
.il
[i
++];
2185 int nral
= NRAL(ftype
);
2186 /* Skip the ifunc index */
2188 for (int j
= 0; j
< nral
; j
++)
2190 /* Here we assume we have no charge groups;
2191 * this has been checked above.
2193 int aj
= ril_intermol
.il
[i
+ j
];
2194 check_link(link
, cg_gl
, aj
);
2196 i
+= nral_rt(ftype
);
2200 if (link
->index
[cg_gl
+1] - link
->index
[cg_gl
] > 0)
2202 SET_CGINFO_BOND_INTER(cgi_mb
->cginfo
[cg
]);
2207 cg_offset
+= cgs
.nr
;
2209 int nlink_mol
= link
->index
[cg_offset
] - link
->index
[cg_offset
- cgs
.nr
];
2213 fprintf(debug
, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt
.name
, cgs
.nr
, nlink_mol
);
2216 if (molb
.nmol
> mol
)
2218 /* Copy the data for the rest of the molecules in this block */
2219 link
->nalloc_a
+= (molb
.nmol
- mol
)*nlink_mol
;
2220 srenew(link
->a
, link
->nalloc_a
);
2221 for (; mol
< molb
.nmol
; mol
++)
2223 for (int cg
= 0; cg
< cgs
.nr
; cg
++)
2225 int cg_gl
= cg_offset
+ cg
;
2226 link
->index
[cg_gl
+ 1] =
2227 link
->index
[cg_gl
+ 1 - cgs
.nr
] + nlink_mol
;
2228 for (int j
= link
->index
[cg_gl
]; j
< link
->index
[cg_gl
+1]; j
++)
2230 link
->a
[j
] = link
->a
[j
- nlink_mol
] + cgs
.nr
;
2232 if (link
->index
[cg_gl
+1] - link
->index
[cg_gl
] > 0 &&
2233 cg_gl
- cgi_mb
->cg_start
< cgi_mb
->cg_mod
)
2235 SET_CGINFO_BOND_INTER(cgi_mb
->cginfo
[cg_gl
- cgi_mb
->cg_start
]);
2239 cg_offset
+= cgs
.nr
;
2246 fprintf(debug
, "Of the %d charge groups %d are linked via bonded interactions\n", ncg_mtop(mtop
), ncgi
);
2257 } bonded_distance_t
;
2259 /*! \brief Compare distance^2 \p r2 against the distance in \p bd and if larger store it along with \p ftype and atom indices \p a1 and \p a2 */
2260 static void update_max_bonded_distance(real r2
, int ftype
, int a1
, int a2
,
2261 bonded_distance_t
*bd
)
2272 /*! \brief Set the distance, function type and atom indices for the longest distance between charge-groups of molecule type \p molt for two-body and multi-body bonded interactions */
2273 static void bonded_cg_distance_mol(const gmx_moltype_t
*molt
,
2274 const std::vector
<int> &at2cg
,
2275 gmx_bool bBCheck
, gmx_bool bExcl
, rvec
*cg_cm
,
2276 bonded_distance_t
*bd_2b
,
2277 bonded_distance_t
*bd_mb
)
2279 for (int ftype
= 0; ftype
< F_NRE
; ftype
++)
2281 if (dd_check_ftype(ftype
, bBCheck
, FALSE
, FALSE
))
2283 const auto &il
= molt
->ilist
[ftype
];
2284 int nral
= NRAL(ftype
);
2287 for (int i
= 0; i
< il
.size(); i
+= 1+nral
)
2289 for (int ai
= 0; ai
< nral
; ai
++)
2291 int cgi
= at2cg
[il
.iatoms
[i
+1+ai
]];
2292 for (int aj
= ai
+ 1; aj
< nral
; aj
++)
2294 int cgj
= at2cg
[il
.iatoms
[i
+1+aj
]];
2297 real rij2
= distance2(cg_cm
[cgi
], cg_cm
[cgj
]);
2299 update_max_bonded_distance(rij2
, ftype
,
2302 (nral
== 2) ? bd_2b
: bd_mb
);
2312 const t_blocka
*excls
= &molt
->excls
;
2313 for (int ai
= 0; ai
< excls
->nr
; ai
++)
2315 int cgi
= at2cg
[ai
];
2316 for (int j
= excls
->index
[ai
]; j
< excls
->index
[ai
+1]; j
++)
2318 int cgj
= at2cg
[excls
->a
[j
]];
2321 real rij2
= distance2(cg_cm
[cgi
], cg_cm
[cgj
]);
2323 /* There is no function type for exclusions, use -1 */
2324 update_max_bonded_distance(rij2
, -1, ai
, excls
->a
[j
], bd_2b
);
2331 /*! \brief Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions */
2332 static void bonded_distance_intermol(const InteractionLists
&ilists_intermol
,
2334 const rvec
*x
, int ePBC
, const matrix box
,
2335 bonded_distance_t
*bd_2b
,
2336 bonded_distance_t
*bd_mb
)
2340 set_pbc(&pbc
, ePBC
, box
);
2342 for (int ftype
= 0; ftype
< F_NRE
; ftype
++)
2344 if (dd_check_ftype(ftype
, bBCheck
, FALSE
, FALSE
))
2346 const auto &il
= ilists_intermol
[ftype
];
2347 int nral
= NRAL(ftype
);
2349 /* No nral>1 check here, since intermol interactions always
2350 * have nral>=2 (and the code is also correct for nral=1).
2352 for (int i
= 0; i
< il
.size(); i
+= 1+nral
)
2354 for (int ai
= 0; ai
< nral
; ai
++)
2356 int atom_i
= il
.iatoms
[i
+ 1 + ai
];
2358 for (int aj
= ai
+ 1; aj
< nral
; aj
++)
2363 int atom_j
= il
.iatoms
[i
+ 1 + aj
];
2365 pbc_dx(&pbc
, x
[atom_i
], x
[atom_j
], dx
);
2369 update_max_bonded_distance(rij2
, ftype
,
2371 (nral
== 2) ? bd_2b
: bd_mb
);
2379 //! Returns whether \p molt has at least one virtual site
2380 static bool moltypeHasVsite(const gmx_moltype_t
&molt
)
2382 bool hasVsite
= false;
2383 for (int i
= 0; i
< F_NRE
; i
++)
2385 if ((interaction_function
[i
].flags
& IF_VSITE
) &&
2386 molt
.ilist
[i
].size() > 0)
2395 //! Compute charge group centers of mass for molecule \p molt
2396 static void get_cgcm_mol(const gmx_moltype_t
*molt
,
2397 const gmx_ffparams_t
*ffparams
,
2398 int ePBC
, t_graph
*graph
, const matrix box
,
2399 const rvec
*x
, rvec
*xs
, rvec
*cg_cm
)
2403 if (ePBC
!= epbcNONE
)
2405 mk_mshift(nullptr, graph
, ePBC
, box
, x
);
2407 shift_x(graph
, box
, x
, xs
);
2408 /* By doing an extra mk_mshift the molecules that are broken
2409 * because they were e.g. imported from another software
2410 * will be made whole again. Such are the healing powers
2413 mk_mshift(nullptr, graph
, ePBC
, box
, xs
);
2417 /* We copy the coordinates so the original coordinates remain
2418 * unchanged, just to be 100% sure that we do not affect
2419 * binary reproducibility of simulations.
2421 n
= molt
->cgs
.index
[molt
->cgs
.nr
];
2422 for (i
= 0; i
< n
; i
++)
2424 copy_rvec(x
[i
], xs
[i
]);
2428 if (moltypeHasVsite(*molt
))
2430 /* Convert to old, deprecated format */
2431 t_ilist ilist
[F_NRE
];
2432 for (int ftype
= 0; ftype
< F_NRE
; ftype
++)
2434 if (interaction_function
[ftype
].flags
& IF_VSITE
)
2436 ilist
[ftype
].nr
= molt
->ilist
[ftype
].size();
2437 ilist
[ftype
].iatoms
= const_cast<int *>(molt
->ilist
[ftype
].iatoms
.data());
2441 construct_vsites(nullptr, xs
, 0.0, nullptr,
2442 ffparams
->iparams
.data(), ilist
,
2443 epbcNONE
, TRUE
, nullptr, nullptr);
2446 calc_cgcm(nullptr, 0, molt
->cgs
.nr
, &molt
->cgs
, xs
, cg_cm
);
2449 void dd_bonded_cg_distance(const gmx::MDLogger
&mdlog
,
2450 const gmx_mtop_t
*mtop
,
2451 const t_inputrec
*ir
,
2452 const rvec
*x
, const matrix box
,
2454 real
*r_2b
, real
*r_mb
)
2456 gmx_bool bExclRequired
;
2460 bonded_distance_t bd_2b
= { 0, -1, -1, -1 };
2461 bonded_distance_t bd_mb
= { 0, -1, -1, -1 };
2463 bExclRequired
= inputrecExclForces(ir
);
2468 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
2470 const gmx_moltype_t
&molt
= mtop
->moltype
[molb
.type
];
2471 if (molt
.cgs
.nr
== 1 || molb
.nmol
== 0)
2473 at_offset
+= molb
.nmol
*molt
.atoms
.nr
;
2477 if (ir
->ePBC
!= epbcNONE
)
2479 mk_graph_moltype(molt
, &graph
);
2482 std::vector
<int> at2cg
= make_at2cg(molt
.cgs
);
2483 snew(xs
, molt
.atoms
.nr
);
2484 snew(cg_cm
, molt
.cgs
.nr
);
2485 for (int mol
= 0; mol
< molb
.nmol
; mol
++)
2487 get_cgcm_mol(&molt
, &mtop
->ffparams
, ir
->ePBC
, &graph
, box
,
2488 x
+at_offset
, xs
, cg_cm
);
2490 bonded_distance_t bd_mol_2b
= { 0, -1, -1, -1 };
2491 bonded_distance_t bd_mol_mb
= { 0, -1, -1, -1 };
2493 bonded_cg_distance_mol(&molt
, at2cg
, bBCheck
, bExclRequired
, cg_cm
,
2494 &bd_mol_2b
, &bd_mol_mb
);
2496 /* Process the mol data adding the atom index offset */
2497 update_max_bonded_distance(bd_mol_2b
.r2
, bd_mol_2b
.ftype
,
2498 at_offset
+ bd_mol_2b
.a1
,
2499 at_offset
+ bd_mol_2b
.a2
,
2501 update_max_bonded_distance(bd_mol_mb
.r2
, bd_mol_mb
.ftype
,
2502 at_offset
+ bd_mol_mb
.a1
,
2503 at_offset
+ bd_mol_mb
.a2
,
2506 at_offset
+= molt
.atoms
.nr
;
2510 if (ir
->ePBC
!= epbcNONE
)
2517 if (mtop
->bIntermolecularInteractions
)
2519 if (ncg_mtop(mtop
) < mtop
->natoms
)
2521 gmx_fatal(FARGS
, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
2524 GMX_RELEASE_ASSERT(mtop
->intermolecular_ilist
, "We should have an ilist when intermolecular interactions are on");
2526 bonded_distance_intermol(*mtop
->intermolecular_ilist
,
2532 *r_2b
= sqrt(bd_2b
.r2
);
2533 *r_mb
= sqrt(bd_mb
.r2
);
2535 if (*r_2b
> 0 || *r_mb
> 0)
2537 GMX_LOG(mdlog
.info
).appendText("Initial maximum distances in bonded interactions:");
2540 GMX_LOG(mdlog
.info
).appendTextFormatted(
2541 " two-body bonded interactions: %5.3f nm, %s, atoms %d %d",
2542 *r_2b
, (bd_2b
.ftype
>= 0) ? interaction_function
[bd_2b
.ftype
].longname
: "Exclusion",
2543 bd_2b
.a1
+ 1, bd_2b
.a2
+ 1);
2547 GMX_LOG(mdlog
.info
).appendTextFormatted(
2548 " multi-body bonded interactions: %5.3f nm, %s, atoms %d %d",
2549 *r_mb
, interaction_function
[bd_mb
.ftype
].longname
,
2550 bd_mb
.a1
+ 1, bd_mb
.a2
+ 1);