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50 #include "gromacs/commandline/filenm.h"
51 #include "gromacs/compat/make_unique.h"
52 #include "gromacs/domdec/domdec.h"
53 #include "gromacs/domdec/domdec_struct.h"
54 #include "gromacs/ewald/ewald.h"
55 #include "gromacs/ewald/ewald-utils.h"
56 #include "gromacs/fileio/filetypes.h"
57 #include "gromacs/gmxlib/network.h"
58 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
59 #include "gromacs/gpu_utils/gpu_utils.h"
60 #include "gromacs/hardware/hw_info.h"
61 #include "gromacs/listed-forces/gpubonded.h"
62 #include "gromacs/listed-forces/manage-threading.h"
63 #include "gromacs/listed-forces/pairs.h"
64 #include "gromacs/math/functions.h"
65 #include "gromacs/math/units.h"
66 #include "gromacs/math/utilities.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/mdlib/force.h"
69 #include "gromacs/mdlib/forcerec-threading.h"
70 #include "gromacs/mdlib/gmx_omp_nthreads.h"
71 #include "gromacs/mdlib/md_support.h"
72 #include "gromacs/mdlib/nb_verlet.h"
73 #include "gromacs/mdlib/nbnxn_atomdata.h"
74 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
75 #include "gromacs/mdlib/nbnxn_grid.h"
76 #include "gromacs/mdlib/nbnxn_internal.h"
77 #include "gromacs/mdlib/nbnxn_search.h"
78 #include "gromacs/mdlib/nbnxn_simd.h"
79 #include "gromacs/mdlib/nbnxn_tuning.h"
80 #include "gromacs/mdlib/nbnxn_util.h"
81 #include "gromacs/mdlib/ns.h"
82 #include "gromacs/mdlib/qmmm.h"
83 #include "gromacs/mdlib/rf_util.h"
84 #include "gromacs/mdlib/sim_util.h"
85 #include "gromacs/mdlib/wall.h"
86 #include "gromacs/mdtypes/commrec.h"
87 #include "gromacs/mdtypes/fcdata.h"
88 #include "gromacs/mdtypes/group.h"
89 #include "gromacs/mdtypes/iforceprovider.h"
90 #include "gromacs/mdtypes/inputrec.h"
91 #include "gromacs/mdtypes/md_enums.h"
92 #include "gromacs/pbcutil/ishift.h"
93 #include "gromacs/pbcutil/pbc.h"
94 #include "gromacs/simd/simd.h"
95 #include "gromacs/tables/forcetable.h"
96 #include "gromacs/topology/mtop_util.h"
97 #include "gromacs/trajectory/trajectoryframe.h"
98 #include "gromacs/utility/cstringutil.h"
99 #include "gromacs/utility/exceptions.h"
100 #include "gromacs/utility/fatalerror.h"
101 #include "gromacs/utility/gmxassert.h"
102 #include "gromacs/utility/logger.h"
103 #include "gromacs/utility/physicalnodecommunicator.h"
104 #include "gromacs/utility/pleasecite.h"
105 #include "gromacs/utility/smalloc.h"
106 #include "gromacs/utility/strconvert.h"
108 #include "nbnxn_gpu_jit_support.h"
110 t_forcerec
*mk_forcerec()
119 static real
*mk_nbfp(const gmx_ffparams_t
*idef
, gmx_bool bBHAM
)
127 snew(nbfp
, 3*atnr
*atnr
);
128 for (i
= k
= 0; (i
< atnr
); i
++)
130 for (j
= 0; (j
< atnr
); j
++, k
++)
132 BHAMA(nbfp
, atnr
, i
, j
) = idef
->iparams
[k
].bham
.a
;
133 BHAMB(nbfp
, atnr
, i
, j
) = idef
->iparams
[k
].bham
.b
;
134 /* nbfp now includes the 6.0 derivative prefactor */
135 BHAMC(nbfp
, atnr
, i
, j
) = idef
->iparams
[k
].bham
.c
*6.0;
141 snew(nbfp
, 2*atnr
*atnr
);
142 for (i
= k
= 0; (i
< atnr
); i
++)
144 for (j
= 0; (j
< atnr
); j
++, k
++)
146 /* nbfp now includes the 6.0/12.0 derivative prefactors */
147 C6(nbfp
, atnr
, i
, j
) = idef
->iparams
[k
].lj
.c6
*6.0;
148 C12(nbfp
, atnr
, i
, j
) = idef
->iparams
[k
].lj
.c12
*12.0;
156 static real
*make_ljpme_c6grid(const gmx_ffparams_t
*idef
, t_forcerec
*fr
)
159 real c6
, c6i
, c6j
, c12i
, c12j
, epsi
, epsj
, sigmai
, sigmaj
;
162 /* For LJ-PME simulations, we correct the energies with the reciprocal space
163 * inside of the cut-off. To do this the non-bonded kernels needs to have
164 * access to the C6-values used on the reciprocal grid in pme.c
168 snew(grid
, 2*atnr
*atnr
);
169 for (i
= k
= 0; (i
< atnr
); i
++)
171 for (j
= 0; (j
< atnr
); j
++, k
++)
173 c6i
= idef
->iparams
[i
*(atnr
+1)].lj
.c6
;
174 c12i
= idef
->iparams
[i
*(atnr
+1)].lj
.c12
;
175 c6j
= idef
->iparams
[j
*(atnr
+1)].lj
.c6
;
176 c12j
= idef
->iparams
[j
*(atnr
+1)].lj
.c12
;
177 c6
= std::sqrt(c6i
* c6j
);
178 if (fr
->ljpme_combination_rule
== eljpmeLB
179 && !gmx_numzero(c6
) && !gmx_numzero(c12i
) && !gmx_numzero(c12j
))
181 sigmai
= gmx::sixthroot(c12i
/ c6i
);
182 sigmaj
= gmx::sixthroot(c12j
/ c6j
);
183 epsi
= c6i
* c6i
/ c12i
;
184 epsj
= c6j
* c6j
/ c12j
;
185 c6
= std::sqrt(epsi
* epsj
) * gmx::power6(0.5*(sigmai
+sigmaj
));
187 /* Store the elements at the same relative positions as C6 in nbfp in order
188 * to simplify access in the kernels
190 grid
[2*(atnr
*i
+j
)] = c6
*6.0;
196 static real
*mk_nbfp_combination_rule(const gmx_ffparams_t
*idef
, int comb_rule
)
200 real c6i
, c6j
, c12i
, c12j
, epsi
, epsj
, sigmai
, sigmaj
;
204 snew(nbfp
, 2*atnr
*atnr
);
205 for (i
= 0; i
< atnr
; ++i
)
207 for (j
= 0; j
< atnr
; ++j
)
209 c6i
= idef
->iparams
[i
*(atnr
+1)].lj
.c6
;
210 c12i
= idef
->iparams
[i
*(atnr
+1)].lj
.c12
;
211 c6j
= idef
->iparams
[j
*(atnr
+1)].lj
.c6
;
212 c12j
= idef
->iparams
[j
*(atnr
+1)].lj
.c12
;
213 c6
= std::sqrt(c6i
* c6j
);
214 c12
= std::sqrt(c12i
* c12j
);
215 if (comb_rule
== eCOMB_ARITHMETIC
216 && !gmx_numzero(c6
) && !gmx_numzero(c12
))
218 sigmai
= gmx::sixthroot(c12i
/ c6i
);
219 sigmaj
= gmx::sixthroot(c12j
/ c6j
);
220 epsi
= c6i
* c6i
/ c12i
;
221 epsj
= c6j
* c6j
/ c12j
;
222 c6
= std::sqrt(epsi
* epsj
) * gmx::power6(0.5*(sigmai
+sigmaj
));
223 c12
= std::sqrt(epsi
* epsj
) * gmx::power12(0.5*(sigmai
+sigmaj
));
225 C6(nbfp
, atnr
, i
, j
) = c6
*6.0;
226 C12(nbfp
, atnr
, i
, j
) = c12
*12.0;
232 /* This routine sets fr->solvent_opt to the most common solvent in the
233 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
234 * the fr->solvent_type array with the correct type (or esolNO).
236 * Charge groups that fulfill the conditions but are not identical to the
237 * most common one will be marked as esolNO in the solvent_type array.
239 * TIP3p is identical to SPC for these purposes, so we call it
240 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
242 * NOTE: QM particle should not
243 * become an optimized solvent. Not even if there is only one charge
253 } solvent_parameters_t
;
256 check_solvent_cg(const gmx_moltype_t
*molt
,
259 const unsigned char *qm_grpnr
,
260 const t_grps
*qm_grps
,
262 int *n_solvent_parameters
,
263 solvent_parameters_t
**solvent_parameters_p
,
273 real tmp_charge
[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
274 int tmp_vdwtype
[4] = { 0 }; /* init to zero to make gcc4.8 happy */
277 solvent_parameters_t
*solvent_parameters
;
279 /* We use a list with parameters for each solvent type.
280 * Every time we discover a new molecule that fulfills the basic
281 * conditions for a solvent we compare with the previous entries
282 * in these lists. If the parameters are the same we just increment
283 * the counter for that type, and otherwise we create a new type
284 * based on the current molecule.
286 * Once we've finished going through all molecules we check which
287 * solvent is most common, and mark all those molecules while we
288 * clear the flag on all others.
291 solvent_parameters
= *solvent_parameters_p
;
293 /* Mark the cg first as non optimized */
296 /* Check if this cg has no exclusions with atoms in other charge groups
297 * and all atoms inside the charge group excluded.
298 * We only have 3 or 4 atom solvent loops.
300 if (GET_CGINFO_EXCL_INTER(cginfo
) ||
301 !GET_CGINFO_EXCL_INTRA(cginfo
))
306 /* Get the indices of the first atom in this charge group */
307 j0
= molt
->cgs
.index
[cg0
];
308 j1
= molt
->cgs
.index
[cg0
+1];
310 /* Number of atoms in our molecule */
316 "Moltype '%s': there are %d atoms in this charge group\n",
320 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
323 if (nj
< 3 || nj
> 4)
328 /* Check if we are doing QM on this group */
330 if (qm_grpnr
!= nullptr)
332 for (j
= j0
; j
< j1
&& !qm
; j
++)
334 qm
= (qm_grpnr
[j
] < qm_grps
->nr
- 1);
337 /* Cannot use solvent optimization with QM */
343 atom
= molt
->atoms
.atom
;
345 /* Still looks like a solvent, time to check parameters */
347 /* If it is perturbed (free energy) we can't use the solvent loops,
348 * so then we just skip to the next molecule.
352 for (j
= j0
; j
< j1
&& !perturbed
; j
++)
354 perturbed
= PERTURBED(atom
[j
]);
362 /* Now it's only a question if the VdW and charge parameters
363 * are OK. Before doing the check we compare and see if they are
364 * identical to a possible previous solvent type.
365 * First we assign the current types and charges.
367 for (j
= 0; j
< nj
; j
++)
369 tmp_vdwtype
[j
] = atom
[j0
+j
].type
;
370 tmp_charge
[j
] = atom
[j0
+j
].q
;
373 /* Does it match any previous solvent type? */
374 for (k
= 0; k
< *n_solvent_parameters
; k
++)
379 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
380 if ( (solvent_parameters
[k
].model
== esolSPC
&& nj
!= 3) ||
381 (solvent_parameters
[k
].model
== esolTIP4P
&& nj
!= 4) )
386 /* Check that types & charges match for all atoms in molecule */
387 for (j
= 0; j
< nj
&& match
; j
++)
389 if (tmp_vdwtype
[j
] != solvent_parameters
[k
].vdwtype
[j
])
393 if (tmp_charge
[j
] != solvent_parameters
[k
].charge
[j
])
400 /* Congratulations! We have a matched solvent.
401 * Flag it with this type for later processing.
404 solvent_parameters
[k
].count
+= nmol
;
406 /* We are done with this charge group */
411 /* If we get here, we have a tentative new solvent type.
412 * Before we add it we must check that it fulfills the requirements
413 * of the solvent optimized loops. First determine which atoms have
416 for (j
= 0; j
< nj
; j
++)
419 tjA
= tmp_vdwtype
[j
];
421 /* Go through all other tpes and see if any have non-zero
422 * VdW parameters when combined with this one.
424 for (k
= 0; k
< fr
->ntype
&& (!has_vdw
[j
]); k
++)
426 /* We already checked that the atoms weren't perturbed,
427 * so we only need to check state A now.
431 has_vdw
[j
] = (has_vdw
[j
] ||
432 (BHAMA(fr
->nbfp
, fr
->ntype
, tjA
, k
) != 0.0) ||
433 (BHAMB(fr
->nbfp
, fr
->ntype
, tjA
, k
) != 0.0) ||
434 (BHAMC(fr
->nbfp
, fr
->ntype
, tjA
, k
) != 0.0));
439 has_vdw
[j
] = (has_vdw
[j
] ||
440 (C6(fr
->nbfp
, fr
->ntype
, tjA
, k
) != 0.0) ||
441 (C12(fr
->nbfp
, fr
->ntype
, tjA
, k
) != 0.0));
446 /* Now we know all we need to make the final check and assignment. */
450 * For this we require thatn all atoms have charge,
451 * the charges on atom 2 & 3 should be the same, and only
452 * atom 1 might have VdW.
456 tmp_charge
[0] != 0 &&
457 tmp_charge
[1] != 0 &&
458 tmp_charge
[2] == tmp_charge
[1])
460 srenew(solvent_parameters
, *n_solvent_parameters
+1);
461 solvent_parameters
[*n_solvent_parameters
].model
= esolSPC
;
462 solvent_parameters
[*n_solvent_parameters
].count
= nmol
;
463 for (k
= 0; k
< 3; k
++)
465 solvent_parameters
[*n_solvent_parameters
].vdwtype
[k
] = tmp_vdwtype
[k
];
466 solvent_parameters
[*n_solvent_parameters
].charge
[k
] = tmp_charge
[k
];
469 *cg_sp
= *n_solvent_parameters
;
470 (*n_solvent_parameters
)++;
475 /* Or could it be a TIP4P?
476 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
477 * Only atom 1 mght have VdW.
482 tmp_charge
[0] == 0 &&
483 tmp_charge
[1] != 0 &&
484 tmp_charge
[2] == tmp_charge
[1] &&
487 srenew(solvent_parameters
, *n_solvent_parameters
+1);
488 solvent_parameters
[*n_solvent_parameters
].model
= esolTIP4P
;
489 solvent_parameters
[*n_solvent_parameters
].count
= nmol
;
490 for (k
= 0; k
< 4; k
++)
492 solvent_parameters
[*n_solvent_parameters
].vdwtype
[k
] = tmp_vdwtype
[k
];
493 solvent_parameters
[*n_solvent_parameters
].charge
[k
] = tmp_charge
[k
];
496 *cg_sp
= *n_solvent_parameters
;
497 (*n_solvent_parameters
)++;
501 *solvent_parameters_p
= solvent_parameters
;
505 check_solvent(FILE * fp
,
506 const gmx_mtop_t
* mtop
,
508 cginfo_mb_t
*cginfo_mb
)
511 const gmx_moltype_t
*molt
;
512 int mol
, cg_mol
, at_offset
, am
, cgm
, i
, nmol_ch
, nmol
;
513 int n_solvent_parameters
;
514 solvent_parameters_t
*solvent_parameters
;
520 fprintf(debug
, "Going to determine what solvent types we have.\n");
523 n_solvent_parameters
= 0;
524 solvent_parameters
= nullptr;
525 /* Allocate temporary array for solvent type */
526 snew(cg_sp
, mtop
->molblock
.size());
529 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
531 molt
= &mtop
->moltype
[mtop
->molblock
[mb
].type
];
533 /* Here we have to loop over all individual molecules
534 * because we need to check for QMMM particles.
536 snew(cg_sp
[mb
], cginfo_mb
[mb
].cg_mod
);
537 nmol_ch
= cginfo_mb
[mb
].cg_mod
/cgs
->nr
;
538 nmol
= mtop
->molblock
[mb
].nmol
/nmol_ch
;
539 for (mol
= 0; mol
< nmol_ch
; mol
++)
542 am
= mol
*cgs
->index
[cgs
->nr
];
543 for (cg_mol
= 0; cg_mol
< cgs
->nr
; cg_mol
++)
545 check_solvent_cg(molt
, cg_mol
, nmol
,
546 mtop
->groups
.grpnr
[egcQMMM
] ?
547 mtop
->groups
.grpnr
[egcQMMM
]+at_offset
+am
: nullptr,
548 &mtop
->groups
.grps
[egcQMMM
],
550 &n_solvent_parameters
, &solvent_parameters
,
551 cginfo_mb
[mb
].cginfo
[cgm
+cg_mol
],
552 &cg_sp
[mb
][cgm
+cg_mol
]);
555 at_offset
+= cgs
->index
[cgs
->nr
];
558 /* Puh! We finished going through all charge groups.
559 * Now find the most common solvent model.
562 /* Most common solvent this far */
564 for (i
= 0; i
< n_solvent_parameters
; i
++)
567 solvent_parameters
[i
].count
> solvent_parameters
[bestsp
].count
)
575 bestsol
= solvent_parameters
[bestsp
].model
;
583 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
585 cgs
= &mtop
->moltype
[mtop
->molblock
[mb
].type
].cgs
;
586 nmol
= (mtop
->molblock
[mb
].nmol
*cgs
->nr
)/cginfo_mb
[mb
].cg_mod
;
587 for (i
= 0; i
< cginfo_mb
[mb
].cg_mod
; i
++)
589 if (cg_sp
[mb
][i
] == bestsp
)
591 SET_CGINFO_SOLOPT(cginfo_mb
[mb
].cginfo
[i
], bestsol
);
596 SET_CGINFO_SOLOPT(cginfo_mb
[mb
].cginfo
[i
], esolNO
);
603 if (bestsol
!= esolNO
&& fp
!= nullptr)
605 fprintf(fp
, "\nEnabling %s-like water optimization for %d molecules.\n\n",
607 solvent_parameters
[bestsp
].count
);
610 sfree(solvent_parameters
);
611 fr
->solvent_opt
= bestsol
;
615 acNONE
= 0, acCONSTRAINT
, acSETTLE
618 static cginfo_mb_t
*init_cginfo_mb(FILE *fplog
, const gmx_mtop_t
*mtop
,
619 t_forcerec
*fr
, gmx_bool bNoSolvOpt
,
620 gmx_bool
*bFEP_NonBonded
,
621 gmx_bool
*bExcl_IntraCGAll_InterCGNone
)
624 const t_blocka
*excl
;
625 const gmx_moltype_t
*molt
;
626 const gmx_molblock_t
*molb
;
627 cginfo_mb_t
*cginfo_mb
;
630 int cg_offset
, a_offset
;
631 int m
, cg
, a0
, a1
, gid
, ai
, j
, aj
, excl_nalloc
;
635 gmx_bool bId
, *bExcl
, bExclIntraAll
, bExclInter
, bHaveVDW
, bHaveQ
, bHavePerturbedAtoms
;
637 snew(cginfo_mb
, mtop
->molblock
.size());
639 snew(type_VDW
, fr
->ntype
);
640 for (ai
= 0; ai
< fr
->ntype
; ai
++)
642 type_VDW
[ai
] = FALSE
;
643 for (j
= 0; j
< fr
->ntype
; j
++)
645 type_VDW
[ai
] = type_VDW
[ai
] ||
647 C6(fr
->nbfp
, fr
->ntype
, ai
, j
) != 0 ||
648 C12(fr
->nbfp
, fr
->ntype
, ai
, j
) != 0;
652 *bFEP_NonBonded
= FALSE
;
653 *bExcl_IntraCGAll_InterCGNone
= TRUE
;
656 snew(bExcl
, excl_nalloc
);
659 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
661 molb
= &mtop
->molblock
[mb
];
662 molt
= &mtop
->moltype
[molb
->type
];
666 /* Check if the cginfo is identical for all molecules in this block.
667 * If so, we only need an array of the size of one molecule.
668 * Otherwise we make an array of #mol times #cgs per molecule.
671 for (m
= 0; m
< molb
->nmol
; m
++)
673 int am
= m
*cgs
->index
[cgs
->nr
];
674 for (cg
= 0; cg
< cgs
->nr
; cg
++)
677 a1
= cgs
->index
[cg
+1];
678 if (getGroupType(mtop
->groups
, egcENER
, a_offset
+am
+a0
) !=
679 getGroupType(mtop
->groups
, egcENER
, a_offset
+a0
))
683 if (mtop
->groups
.grpnr
[egcQMMM
] != nullptr)
685 for (ai
= a0
; ai
< a1
; ai
++)
687 if (mtop
->groups
.grpnr
[egcQMMM
][a_offset
+am
+ai
] !=
688 mtop
->groups
.grpnr
[egcQMMM
][a_offset
+ai
])
697 cginfo_mb
[mb
].cg_start
= cg_offset
;
698 cginfo_mb
[mb
].cg_end
= cg_offset
+ molb
->nmol
*cgs
->nr
;
699 cginfo_mb
[mb
].cg_mod
= (bId
? 1 : molb
->nmol
)*cgs
->nr
;
700 snew(cginfo_mb
[mb
].cginfo
, cginfo_mb
[mb
].cg_mod
);
701 cginfo
= cginfo_mb
[mb
].cginfo
;
703 /* Set constraints flags for constrained atoms */
704 snew(a_con
, molt
->atoms
.nr
);
705 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
707 if (interaction_function
[ftype
].flags
& IF_CONSTRAINT
)
712 for (ia
= 0; ia
< molt
->ilist
[ftype
].size(); ia
+= 1+nral
)
716 for (a
= 0; a
< nral
; a
++)
718 a_con
[molt
->ilist
[ftype
].iatoms
[ia
+1+a
]] =
719 (ftype
== F_SETTLE
? acSETTLE
: acCONSTRAINT
);
725 for (m
= 0; m
< (bId
? 1 : molb
->nmol
); m
++)
728 int am
= m
*cgs
->index
[cgs
->nr
];
729 for (cg
= 0; cg
< cgs
->nr
; cg
++)
732 a1
= cgs
->index
[cg
+1];
734 /* Store the energy group in cginfo */
735 gid
= getGroupType(mtop
->groups
, egcENER
, a_offset
+am
+a0
);
736 SET_CGINFO_GID(cginfo
[cgm
+cg
], gid
);
738 /* Check the intra/inter charge group exclusions */
739 if (a1
-a0
> excl_nalloc
)
741 excl_nalloc
= a1
- a0
;
742 srenew(bExcl
, excl_nalloc
);
744 /* bExclIntraAll: all intra cg interactions excluded
745 * bExclInter: any inter cg interactions excluded
747 bExclIntraAll
= TRUE
;
751 bHavePerturbedAtoms
= FALSE
;
752 for (ai
= a0
; ai
< a1
; ai
++)
754 /* Check VDW and electrostatic interactions */
755 bHaveVDW
= bHaveVDW
|| (type_VDW
[molt
->atoms
.atom
[ai
].type
] ||
756 type_VDW
[molt
->atoms
.atom
[ai
].typeB
]);
757 bHaveQ
= bHaveQ
|| (molt
->atoms
.atom
[ai
].q
!= 0 ||
758 molt
->atoms
.atom
[ai
].qB
!= 0);
760 bHavePerturbedAtoms
= bHavePerturbedAtoms
|| (PERTURBED(molt
->atoms
.atom
[ai
]) != 0);
762 /* Clear the exclusion list for atom ai */
763 for (aj
= a0
; aj
< a1
; aj
++)
765 bExcl
[aj
-a0
] = FALSE
;
767 /* Loop over all the exclusions of atom ai */
768 for (j
= excl
->index
[ai
]; j
< excl
->index
[ai
+1]; j
++)
771 if (aj
< a0
|| aj
>= a1
)
780 /* Check if ai excludes a0 to a1 */
781 for (aj
= a0
; aj
< a1
; aj
++)
785 bExclIntraAll
= FALSE
;
792 SET_CGINFO_CONSTR(cginfo
[cgm
+cg
]);
795 SET_CGINFO_SETTLE(cginfo
[cgm
+cg
]);
803 SET_CGINFO_EXCL_INTRA(cginfo
[cgm
+cg
]);
807 SET_CGINFO_EXCL_INTER(cginfo
[cgm
+cg
]);
809 if (a1
- a0
> MAX_CHARGEGROUP_SIZE
)
811 /* The size in cginfo is currently only read with DD */
812 gmx_fatal(FARGS
, "A charge group has size %d which is larger than the limit of %d atoms", a1
-a0
, MAX_CHARGEGROUP_SIZE
);
816 SET_CGINFO_HAS_VDW(cginfo
[cgm
+cg
]);
820 SET_CGINFO_HAS_Q(cginfo
[cgm
+cg
]);
822 if (bHavePerturbedAtoms
&& fr
->efep
!= efepNO
)
824 SET_CGINFO_FEP(cginfo
[cgm
+cg
]);
825 *bFEP_NonBonded
= TRUE
;
827 /* Store the charge group size */
828 SET_CGINFO_NATOMS(cginfo
[cgm
+cg
], a1
-a0
);
830 if (!bExclIntraAll
|| bExclInter
)
832 *bExcl_IntraCGAll_InterCGNone
= FALSE
;
839 cg_offset
+= molb
->nmol
*cgs
->nr
;
840 a_offset
+= molb
->nmol
*cgs
->index
[cgs
->nr
];
845 /* the solvent optimizer is called after the QM is initialized,
846 * because we don't want to have the QM subsystemto become an
850 check_solvent(fplog
, mtop
, fr
, cginfo_mb
);
852 if (getenv("GMX_NO_SOLV_OPT"))
856 fprintf(fplog
, "Found environment variable GMX_NO_SOLV_OPT.\n"
857 "Disabling all solvent optimization\n");
859 fr
->solvent_opt
= esolNO
;
863 fr
->solvent_opt
= esolNO
;
865 if (!fr
->solvent_opt
)
867 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
869 for (cg
= 0; cg
< cginfo_mb
[mb
].cg_mod
; cg
++)
871 SET_CGINFO_SOLOPT(cginfo_mb
[mb
].cginfo
[cg
], esolNO
);
879 static int *cginfo_expand(int nmb
, cginfo_mb_t
*cgi_mb
)
884 ncg
= cgi_mb
[nmb
-1].cg_end
;
887 for (cg
= 0; cg
< ncg
; cg
++)
889 while (cg
>= cgi_mb
[mb
].cg_end
)
894 cgi_mb
[mb
].cginfo
[(cg
- cgi_mb
[mb
].cg_start
) % cgi_mb
[mb
].cg_mod
];
900 static void done_cginfo_mb(cginfo_mb_t
*cginfo_mb
, int numMolBlocks
)
902 if (cginfo_mb
== nullptr)
906 for (int mb
= 0; mb
< numMolBlocks
; ++mb
)
908 sfree(cginfo_mb
[mb
].cginfo
);
913 /* Sets the sum of charges (squared) and C6 in the system in fr.
914 * Returns whether the system has a net charge.
916 static bool set_chargesum(FILE *log
, t_forcerec
*fr
, const gmx_mtop_t
*mtop
)
918 /*This now calculates sum for q and c6*/
919 double qsum
, q2sum
, q
, c6sum
, c6
;
924 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
926 int nmol
= molb
.nmol
;
927 const t_atoms
*atoms
= &mtop
->moltype
[molb
.type
].atoms
;
928 for (int i
= 0; i
< atoms
->nr
; i
++)
930 q
= atoms
->atom
[i
].q
;
933 c6
= mtop
->ffparams
.iparams
[atoms
->atom
[i
].type
*(mtop
->ffparams
.atnr
+1)].lj
.c6
;
938 fr
->q2sum
[0] = q2sum
;
939 fr
->c6sum
[0] = c6sum
;
941 if (fr
->efep
!= efepNO
)
946 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
948 int nmol
= molb
.nmol
;
949 const t_atoms
*atoms
= &mtop
->moltype
[molb
.type
].atoms
;
950 for (int i
= 0; i
< atoms
->nr
; i
++)
952 q
= atoms
->atom
[i
].qB
;
955 c6
= mtop
->ffparams
.iparams
[atoms
->atom
[i
].typeB
*(mtop
->ffparams
.atnr
+1)].lj
.c6
;
959 fr
->q2sum
[1] = q2sum
;
960 fr
->c6sum
[1] = c6sum
;
965 fr
->qsum
[1] = fr
->qsum
[0];
966 fr
->q2sum
[1] = fr
->q2sum
[0];
967 fr
->c6sum
[1] = fr
->c6sum
[0];
971 if (fr
->efep
== efepNO
)
973 fprintf(log
, "System total charge: %.3f\n", fr
->qsum
[0]);
977 fprintf(log
, "System total charge, top. A: %.3f top. B: %.3f\n",
978 fr
->qsum
[0], fr
->qsum
[1]);
982 /* A cut-off of 1e-4 is used to catch rounding errors due to ascii input */
983 return (std::abs(fr
->qsum
[0]) > 1e-4 ||
984 std::abs(fr
->qsum
[1]) > 1e-4);
987 void update_forcerec(t_forcerec
*fr
, matrix box
)
989 if (fr
->ic
->eeltype
== eelGRF
)
991 calc_rffac(nullptr, fr
->ic
->eeltype
, fr
->ic
->epsilon_r
, fr
->ic
->epsilon_rf
,
992 fr
->ic
->rcoulomb
, fr
->temp
, fr
->zsquare
, box
,
993 &fr
->ic
->k_rf
, &fr
->ic
->c_rf
);
997 void set_avcsixtwelve(FILE *fplog
, t_forcerec
*fr
, const gmx_mtop_t
*mtop
)
999 const t_atoms
*atoms
, *atoms_tpi
;
1000 const t_blocka
*excl
;
1001 int nmolc
, i
, j
, tpi
, tpj
, j1
, j2
, k
, nexcl
, q
;
1002 int64_t npair
, npair_ij
, tmpi
, tmpj
;
1003 double csix
, ctwelve
;
1004 int ntp
, *typecount
;
1007 real
*nbfp_comb
= nullptr;
1013 /* For LJ-PME, we want to correct for the difference between the
1014 * actual C6 values and the C6 values used by the LJ-PME based on
1015 * combination rules. */
1017 if (EVDW_PME(fr
->ic
->vdwtype
))
1019 nbfp_comb
= mk_nbfp_combination_rule(&mtop
->ffparams
,
1020 (fr
->ljpme_combination_rule
== eljpmeLB
) ? eCOMB_ARITHMETIC
: eCOMB_GEOMETRIC
);
1021 for (tpi
= 0; tpi
< ntp
; ++tpi
)
1023 for (tpj
= 0; tpj
< ntp
; ++tpj
)
1025 C6(nbfp_comb
, ntp
, tpi
, tpj
) =
1026 C6(nbfp
, ntp
, tpi
, tpj
) - C6(nbfp_comb
, ntp
, tpi
, tpj
);
1027 C12(nbfp_comb
, ntp
, tpi
, tpj
) = C12(nbfp
, ntp
, tpi
, tpj
);
1032 for (q
= 0; q
< (fr
->efep
== efepNO
? 1 : 2); q
++)
1040 /* Count the types so we avoid natoms^2 operations */
1041 snew(typecount
, ntp
);
1042 gmx_mtop_count_atomtypes(mtop
, q
, typecount
);
1044 for (tpi
= 0; tpi
< ntp
; tpi
++)
1046 for (tpj
= tpi
; tpj
< ntp
; tpj
++)
1048 tmpi
= typecount
[tpi
];
1049 tmpj
= typecount
[tpj
];
1052 npair_ij
= tmpi
*tmpj
;
1056 npair_ij
= tmpi
*(tmpi
- 1)/2;
1060 /* nbfp now includes the 6.0 derivative prefactor */
1061 csix
+= npair_ij
*BHAMC(nbfp
, ntp
, tpi
, tpj
)/6.0;
1065 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1066 csix
+= npair_ij
* C6(nbfp
, ntp
, tpi
, tpj
)/6.0;
1067 ctwelve
+= npair_ij
* C12(nbfp
, ntp
, tpi
, tpj
)/12.0;
1073 /* Subtract the excluded pairs.
1074 * The main reason for substracting exclusions is that in some cases
1075 * some combinations might never occur and the parameters could have
1076 * any value. These unused values should not influence the dispersion
1079 for (const gmx_molblock_t
&molb
: mtop
->molblock
)
1081 int nmol
= molb
.nmol
;
1082 atoms
= &mtop
->moltype
[molb
.type
].atoms
;
1083 excl
= &mtop
->moltype
[molb
.type
].excls
;
1084 for (int i
= 0; (i
< atoms
->nr
); i
++)
1088 tpi
= atoms
->atom
[i
].type
;
1092 tpi
= atoms
->atom
[i
].typeB
;
1094 j1
= excl
->index
[i
];
1095 j2
= excl
->index
[i
+1];
1096 for (j
= j1
; j
< j2
; j
++)
1103 tpj
= atoms
->atom
[k
].type
;
1107 tpj
= atoms
->atom
[k
].typeB
;
1111 /* nbfp now includes the 6.0 derivative prefactor */
1112 csix
-= nmol
*BHAMC(nbfp
, ntp
, tpi
, tpj
)/6.0;
1116 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1117 csix
-= nmol
*C6 (nbfp
, ntp
, tpi
, tpj
)/6.0;
1118 ctwelve
-= nmol
*C12(nbfp
, ntp
, tpi
, tpj
)/12.0;
1128 /* Only correct for the interaction of the test particle
1129 * with the rest of the system.
1132 &mtop
->moltype
[mtop
->molblock
.back().type
].atoms
;
1135 for (size_t mb
= 0; mb
< mtop
->molblock
.size(); mb
++)
1137 const gmx_molblock_t
&molb
= mtop
->molblock
[mb
];
1138 atoms
= &mtop
->moltype
[molb
.type
].atoms
;
1139 for (j
= 0; j
< atoms
->nr
; j
++)
1142 /* Remove the interaction of the test charge group
1145 if (mb
== mtop
->molblock
.size() - 1)
1149 if (mb
== 0 && molb
.nmol
== 1)
1151 gmx_fatal(FARGS
, "Old format tpr with TPI, please generate a new tpr file");
1156 tpj
= atoms
->atom
[j
].type
;
1160 tpj
= atoms
->atom
[j
].typeB
;
1162 for (i
= 0; i
< fr
->n_tpi
; i
++)
1166 tpi
= atoms_tpi
->atom
[i
].type
;
1170 tpi
= atoms_tpi
->atom
[i
].typeB
;
1174 /* nbfp now includes the 6.0 derivative prefactor */
1175 csix
+= nmolc
*BHAMC(nbfp
, ntp
, tpi
, tpj
)/6.0;
1179 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1180 csix
+= nmolc
*C6 (nbfp
, ntp
, tpi
, tpj
)/6.0;
1181 ctwelve
+= nmolc
*C12(nbfp
, ntp
, tpi
, tpj
)/12.0;
1188 if (npair
- nexcl
<= 0 && fplog
)
1190 fprintf(fplog
, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
1196 csix
/= npair
- nexcl
;
1197 ctwelve
/= npair
- nexcl
;
1201 fprintf(debug
, "Counted %d exclusions\n", nexcl
);
1202 fprintf(debug
, "Average C6 parameter is: %10g\n", csix
);
1203 fprintf(debug
, "Average C12 parameter is: %10g\n", ctwelve
);
1205 fr
->avcsix
[q
] = csix
;
1206 fr
->avctwelve
[q
] = ctwelve
;
1209 if (EVDW_PME(fr
->ic
->vdwtype
))
1214 if (fplog
!= nullptr)
1216 if (fr
->eDispCorr
== edispcAllEner
||
1217 fr
->eDispCorr
== edispcAllEnerPres
)
1219 fprintf(fplog
, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1220 fr
->avcsix
[0], fr
->avctwelve
[0]);
1224 fprintf(fplog
, "Long Range LJ corr.: <C6> %10.4e\n", fr
->avcsix
[0]);
1230 static real
calcBuckinghamBMax(FILE *fplog
, const gmx_mtop_t
*mtop
)
1232 const t_atoms
*at1
, *at2
;
1233 int i
, j
, tpi
, tpj
, ntypes
;
1238 fprintf(fplog
, "Determining largest Buckingham b parameter for table\n");
1240 ntypes
= mtop
->ffparams
.atnr
;
1243 real bham_b_max
= 0;
1244 for (size_t mt1
= 0; mt1
< mtop
->moltype
.size(); mt1
++)
1246 at1
= &mtop
->moltype
[mt1
].atoms
;
1247 for (i
= 0; (i
< at1
->nr
); i
++)
1249 tpi
= at1
->atom
[i
].type
;
1252 gmx_fatal(FARGS
, "Atomtype[%d] = %d, maximum = %d", i
, tpi
, ntypes
);
1255 for (size_t mt2
= mt1
; mt2
< mtop
->moltype
.size(); mt2
++)
1257 at2
= &mtop
->moltype
[mt2
].atoms
;
1258 for (j
= 0; (j
< at2
->nr
); j
++)
1260 tpj
= at2
->atom
[j
].type
;
1263 gmx_fatal(FARGS
, "Atomtype[%d] = %d, maximum = %d", j
, tpj
, ntypes
);
1265 b
= mtop
->ffparams
.iparams
[tpi
*ntypes
+ tpj
].bham
.b
;
1270 if ((b
< bmin
) || (bmin
== -1))
1280 fprintf(fplog
, "Buckingham b parameters, min: %g, max: %g\n",
1287 static void make_nbf_tables(FILE *fp
,
1288 const interaction_const_t
*ic
, real rtab
,
1289 const char *tabfn
, char *eg1
, char *eg2
,
1295 if (tabfn
== nullptr)
1299 fprintf(debug
, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1304 sprintf(buf
, "%s", tabfn
);
1307 /* Append the two energy group names */
1308 sprintf(buf
+ strlen(tabfn
) - strlen(ftp2ext(efXVG
)) - 1, "_%s_%s.%s",
1309 eg1
, eg2
, ftp2ext(efXVG
));
1311 nbl
->table_elec_vdw
= make_tables(fp
, ic
, buf
, rtab
, 0);
1312 /* Copy the contents of the table to separate coulomb and LJ tables too,
1313 * to improve cache performance.
1315 /* For performance reasons we want
1316 * the table data to be aligned to 16-byte. The pointers could be freed
1317 * but currently aren't.
1319 snew(nbl
->table_elec
, 1);
1320 nbl
->table_elec
->interaction
= GMX_TABLE_INTERACTION_ELEC
;
1321 nbl
->table_elec
->format
= nbl
->table_elec_vdw
->format
;
1322 nbl
->table_elec
->r
= nbl
->table_elec_vdw
->r
;
1323 nbl
->table_elec
->n
= nbl
->table_elec_vdw
->n
;
1324 nbl
->table_elec
->scale
= nbl
->table_elec_vdw
->scale
;
1325 nbl
->table_elec
->formatsize
= nbl
->table_elec_vdw
->formatsize
;
1326 nbl
->table_elec
->ninteractions
= 1;
1327 nbl
->table_elec
->stride
= nbl
->table_elec
->formatsize
* nbl
->table_elec
->ninteractions
;
1328 snew_aligned(nbl
->table_elec
->data
, nbl
->table_elec
->stride
*(nbl
->table_elec
->n
+1), 32);
1330 snew(nbl
->table_vdw
, 1);
1331 nbl
->table_vdw
->interaction
= GMX_TABLE_INTERACTION_VDWREP_VDWDISP
;
1332 nbl
->table_vdw
->format
= nbl
->table_elec_vdw
->format
;
1333 nbl
->table_vdw
->r
= nbl
->table_elec_vdw
->r
;
1334 nbl
->table_vdw
->n
= nbl
->table_elec_vdw
->n
;
1335 nbl
->table_vdw
->scale
= nbl
->table_elec_vdw
->scale
;
1336 nbl
->table_vdw
->formatsize
= nbl
->table_elec_vdw
->formatsize
;
1337 nbl
->table_vdw
->ninteractions
= 2;
1338 nbl
->table_vdw
->stride
= nbl
->table_vdw
->formatsize
* nbl
->table_vdw
->ninteractions
;
1339 snew_aligned(nbl
->table_vdw
->data
, nbl
->table_vdw
->stride
*(nbl
->table_vdw
->n
+1), 32);
1341 /* NOTE: Using a single i-loop here leads to mix-up of data in table_vdw
1342 * with (at least) gcc 6.2, 6.3 and 6.4 when compiled with -O3 and AVX
1344 for (i
= 0; i
<= nbl
->table_elec_vdw
->n
; i
++)
1346 for (j
= 0; j
< 4; j
++)
1348 nbl
->table_elec
->data
[4*i
+j
] = nbl
->table_elec_vdw
->data
[12*i
+j
];
1351 for (i
= 0; i
<= nbl
->table_elec_vdw
->n
; i
++)
1353 for (j
= 0; j
< 8; j
++)
1355 nbl
->table_vdw
->data
[8*i
+j
] = nbl
->table_elec_vdw
->data
[12*i
+4+j
];
1360 /*!\brief If there's bonded interactions of type \c ftype1 or \c
1361 * ftype2 present in the topology, build an array of the number of
1362 * interactions present for each bonded interaction index found in the
1365 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
1366 * valid type with that parameter.
1368 * \c count will be reallocated as necessary to fit the largest bonded
1369 * interaction index found, and its current size will be returned in
1370 * \c ncount. It will contain zero for every bonded interaction index
1371 * for which no interactions are present in the topology.
1373 static void count_tables(int ftype1
, int ftype2
, const gmx_mtop_t
*mtop
,
1374 int *ncount
, int **count
)
1376 int ftype
, i
, j
, tabnr
;
1378 // Loop over all moleculetypes
1379 for (const gmx_moltype_t
&molt
: mtop
->moltype
)
1381 // Loop over all interaction types
1382 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
1384 // If the current interaction type is one of the types whose tables we're trying to count...
1385 if (ftype
== ftype1
|| ftype
== ftype2
)
1387 const InteractionList
&il
= molt
.ilist
[ftype
];
1388 const int stride
= 1 + NRAL(ftype
);
1389 // ... and there are actually some interactions for this type
1390 for (i
= 0; i
< il
.size(); i
+= stride
)
1392 // Find out which table index the user wanted
1393 tabnr
= mtop
->ffparams
.iparams
[il
.iatoms
[i
]].tab
.table
;
1396 gmx_fatal(FARGS
, "A bonded table number is smaller than 0: %d\n", tabnr
);
1398 // Make room for this index in the data structure
1399 if (tabnr
>= *ncount
)
1401 srenew(*count
, tabnr
+1);
1402 for (j
= *ncount
; j
< tabnr
+1; j
++)
1408 // Record that this table index is used and must have a valid file
1416 /*!\brief If there's bonded interactions of flavour \c tabext and type
1417 * \c ftype1 or \c ftype2 present in the topology, seek them in the
1418 * list of filenames passed to mdrun, and make bonded tables from
1421 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
1422 * valid type with that parameter.
1424 * A fatal error occurs if no matching filename is found.
1426 static bondedtable_t
*make_bonded_tables(FILE *fplog
,
1427 int ftype1
, int ftype2
,
1428 const gmx_mtop_t
*mtop
,
1429 gmx::ArrayRef
<const std::string
> tabbfnm
,
1439 count_tables(ftype1
, ftype2
, mtop
, &ncount
, &count
);
1441 // Are there any relevant tabulated bond interactions?
1445 for (int i
= 0; i
< ncount
; i
++)
1447 // Do any interactions exist that requires this table?
1450 // This pattern enforces the current requirement that
1451 // table filenames end in a characteristic sequence
1452 // before the file type extension, and avoids table 13
1453 // being recognized and used for table 1.
1454 std::string patternToFind
= gmx::formatString("_%s%d.%s", tabext
, i
, ftp2ext(efXVG
));
1455 bool madeTable
= false;
1456 for (gmx::index j
= 0; j
< tabbfnm
.size() && !madeTable
; ++j
)
1458 if (gmx::endsWith(tabbfnm
[j
], patternToFind
))
1460 // Finally read the table from the file found
1461 tab
[i
] = make_bonded_table(fplog
, tabbfnm
[j
].c_str(), NRAL(ftype1
)-2);
1467 bool isPlural
= (ftype2
!= -1);
1468 gmx_fatal(FARGS
, "Tabulated interaction of type '%s%s%s' with index %d cannot be used because no table file whose name matched '%s' was passed via the gmx mdrun -tableb command-line option.",
1469 interaction_function
[ftype1
].longname
,
1470 isPlural
? "' or '" : "",
1471 isPlural
? interaction_function
[ftype2
].longname
: "",
1473 patternToFind
.c_str());
1483 void forcerec_set_ranges(t_forcerec
*fr
,
1484 int ncg_home
, int ncg_force
,
1486 int natoms_force_constr
, int natoms_f_novirsum
)
1491 /* fr->ncg_force is unused in the standard code,
1492 * but it can be useful for modified code dealing with charge groups.
1494 fr
->ncg_force
= ncg_force
;
1495 fr
->natoms_force
= natoms_force
;
1496 fr
->natoms_force_constr
= natoms_force_constr
;
1498 if (fr
->natoms_force_constr
> fr
->nalloc_force
)
1500 fr
->nalloc_force
= over_alloc_dd(fr
->natoms_force_constr
);
1503 if (fr
->haveDirectVirialContributions
)
1505 fr
->forceBufferForDirectVirialContributions
->resize(natoms_f_novirsum
);
1509 static real
cutoff_inf(real cutoff
)
1513 cutoff
= GMX_CUTOFF_INF
;
1519 gmx_bool
can_use_allvsall(const t_inputrec
*ir
, gmx_bool bPrintNote
, const t_commrec
*cr
, FILE *fp
)
1526 ir
->rcoulomb
== 0 &&
1528 ir
->ePBC
== epbcNONE
&&
1529 ir
->vdwtype
== evdwCUT
&&
1530 ir
->coulombtype
== eelCUT
&&
1531 ir
->efep
== efepNO
&&
1532 getenv("GMX_NO_ALLVSALL") == nullptr
1535 if (bAllvsAll
&& ir
->opts
.ngener
> 1)
1537 const char *note
= "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
1543 fprintf(fp
, "\n%s\n", note
);
1549 if (bAllvsAll
&& fp
&& MASTER(cr
))
1551 fprintf(fp
, "\nUsing SIMD all-vs-all kernels.\n\n");
1558 gmx_bool
nbnxn_simd_supported(const gmx::MDLogger
&mdlog
,
1559 const t_inputrec
*ir
)
1561 if (ir
->vdwtype
== evdwPME
&& ir
->ljpme_combination_rule
== eljpmeLB
)
1563 /* LJ PME with LB combination rule does 7 mesh operations.
1564 * This so slow that we don't compile SIMD non-bonded kernels
1566 GMX_LOG(mdlog
.warning
).asParagraph().appendText("LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels");
1574 static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused
*ir
,
1577 const gmx_hw_info_t gmx_unused
&hardwareInfo
)
1579 *kernel_type
= nbnxnk4x4_PlainC
;
1580 *ewald_excl
= ewaldexclTable
;
1584 #ifdef GMX_NBNXN_SIMD_4XN
1585 *kernel_type
= nbnxnk4xN_SIMD_4xN
;
1587 #ifdef GMX_NBNXN_SIMD_2XNN
1588 *kernel_type
= nbnxnk4xN_SIMD_2xNN
;
1591 #if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
1592 /* We need to choose if we want 2x(N+N) or 4xN kernels.
1593 * This is based on the SIMD acceleration choice and CPU information
1594 * detected at runtime.
1596 * 4xN calculates more (zero) interactions, but has less pair-search
1597 * work and much better kernel instruction scheduling.
1599 * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
1600 * which doesn't have FMA, both the analytical and tabulated Ewald
1601 * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
1602 * 2x(4+4) because it results in significantly fewer pairs.
1603 * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
1604 * 10% with HT, 50% without HT. As we currently don't detect the actual
1605 * use of HT, use 4x8 to avoid a potential performance hit.
1606 * On Intel Haswell 4x8 is always faster.
1608 *kernel_type
= nbnxnk4xN_SIMD_4xN
;
1610 #if !GMX_SIMD_HAVE_FMA
1611 if (EEL_PME_EWALD(ir
->coulombtype
) ||
1612 EVDW_PME(ir
->vdwtype
))
1614 /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
1615 * There are enough instructions to make 2x(4+4) efficient.
1617 *kernel_type
= nbnxnk4xN_SIMD_2xNN
;
1620 if (hardwareInfo
.haveAmdZenCpu
)
1622 /* One 256-bit FMA per cycle makes 2xNN faster */
1623 *kernel_type
= nbnxnk4xN_SIMD_2xNN
;
1625 #endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
1628 if (getenv("GMX_NBNXN_SIMD_4XN") != nullptr)
1630 #ifdef GMX_NBNXN_SIMD_4XN
1631 *kernel_type
= nbnxnk4xN_SIMD_4xN
;
1633 gmx_fatal(FARGS
, "SIMD 4xN kernels requested, but GROMACS has been compiled without support for these kernels");
1636 if (getenv("GMX_NBNXN_SIMD_2XNN") != nullptr)
1638 #ifdef GMX_NBNXN_SIMD_2XNN
1639 *kernel_type
= nbnxnk4xN_SIMD_2xNN
;
1641 gmx_fatal(FARGS
, "SIMD 2x(N+N) kernels requested, but GROMACS has been compiled without support for these kernels");
1645 /* Analytical Ewald exclusion correction is only an option in
1647 * Since table lookup's don't parallelize with SIMD, analytical
1648 * will probably always be faster for a SIMD width of 8 or more.
1649 * With FMA analytical is sometimes faster for a width if 4 as well.
1650 * In single precision, this is faster on Bulldozer.
1652 #if GMX_SIMD_REAL_WIDTH >= 8 || \
1653 (GMX_SIMD_REAL_WIDTH >= 4 && GMX_SIMD_HAVE_FMA && !GMX_DOUBLE)
1654 /* On AMD Zen, tabulated Ewald kernels are faster on all 4 combinations
1655 * of single or double precision and 128 or 256-bit AVX2.
1657 if (!hardwareInfo
.haveAmdZenCpu
)
1659 *ewald_excl
= ewaldexclAnalytical
;
1662 if (getenv("GMX_NBNXN_EWALD_TABLE") != nullptr)
1664 *ewald_excl
= ewaldexclTable
;
1666 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != nullptr)
1668 *ewald_excl
= ewaldexclAnalytical
;
1676 const char *lookup_nbnxn_kernel_name(int kernel_type
)
1678 const char *returnvalue
= nullptr;
1679 switch (kernel_type
)
1682 returnvalue
= "not set";
1684 case nbnxnk4x4_PlainC
:
1685 returnvalue
= "plain C";
1687 case nbnxnk4xN_SIMD_4xN
:
1688 case nbnxnk4xN_SIMD_2xNN
:
1690 returnvalue
= "SIMD";
1692 returnvalue
= "not available";
1695 case nbnxnk8x8x8_GPU
: returnvalue
= "GPU"; break;
1696 case nbnxnk8x8x8_PlainC
: returnvalue
= "plain C"; break;
1700 gmx_fatal(FARGS
, "Illegal kernel type selected");
1705 static void pick_nbnxn_kernel(const gmx::MDLogger
&mdlog
,
1706 gmx_bool use_simd_kernels
,
1707 const gmx_hw_info_t
&hardwareInfo
,
1709 EmulateGpuNonbonded emulateGpu
,
1710 const t_inputrec
*ir
,
1713 gmx_bool bDoNonbonded
)
1715 assert(kernel_type
);
1717 *kernel_type
= nbnxnkNotSet
;
1718 *ewald_excl
= ewaldexclTable
;
1720 if (emulateGpu
== EmulateGpuNonbonded::Yes
)
1722 *kernel_type
= nbnxnk8x8x8_PlainC
;
1726 GMX_LOG(mdlog
.warning
).asParagraph().appendText("Emulating a GPU run on the CPU (slow)");
1731 *kernel_type
= nbnxnk8x8x8_GPU
;
1734 if (*kernel_type
== nbnxnkNotSet
)
1736 if (use_simd_kernels
&&
1737 nbnxn_simd_supported(mdlog
, ir
))
1739 pick_nbnxn_kernel_cpu(ir
, kernel_type
, ewald_excl
, hardwareInfo
);
1743 *kernel_type
= nbnxnk4x4_PlainC
;
1749 GMX_LOG(mdlog
.info
).asParagraph().appendTextFormatted(
1750 "Using %s %dx%d nonbonded short-range kernels",
1751 lookup_nbnxn_kernel_name(*kernel_type
),
1752 nbnxn_kernel_to_cluster_i_size(*kernel_type
),
1753 nbnxn_kernel_to_cluster_j_size(*kernel_type
));
1755 if (nbnxnk4x4_PlainC
== *kernel_type
||
1756 nbnxnk8x8x8_PlainC
== *kernel_type
)
1758 GMX_LOG(mdlog
.warning
).asParagraph().appendTextFormatted(
1759 "WARNING: Using the slow %s kernels. This should\n"
1760 "not happen during routine usage on supported platforms.",
1761 lookup_nbnxn_kernel_name(*kernel_type
));
1766 /*! \brief Print Coulomb Ewald citations and set ewald coefficients */
1767 static void initCoulombEwaldParameters(FILE *fp
, const t_inputrec
*ir
,
1768 bool systemHasNetCharge
,
1769 interaction_const_t
*ic
)
1771 if (!EEL_PME_EWALD(ir
->coulombtype
))
1778 fprintf(fp
, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
1780 if (ir
->coulombtype
== eelP3M_AD
)
1782 please_cite(fp
, "Hockney1988");
1783 please_cite(fp
, "Ballenegger2012");
1787 please_cite(fp
, "Essmann95a");
1790 if (ir
->ewald_geometry
== eewg3DC
)
1794 fprintf(fp
, "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
1795 systemHasNetCharge
? " and net charge" : "");
1797 please_cite(fp
, "In-Chul99a");
1798 if (systemHasNetCharge
)
1800 please_cite(fp
, "Ballenegger2009");
1805 ic
->ewaldcoeff_q
= calc_ewaldcoeff_q(ir
->rcoulomb
, ir
->ewald_rtol
);
1808 fprintf(fp
, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
1809 1/ic
->ewaldcoeff_q
);
1812 if (ic
->coulomb_modifier
== eintmodPOTSHIFT
)
1814 GMX_RELEASE_ASSERT(ic
->rcoulomb
!= 0, "Cutoff radius cannot be zero");
1815 ic
->sh_ewald
= std::erfc(ic
->ewaldcoeff_q
*ic
->rcoulomb
) / ic
->rcoulomb
;
1823 /*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
1824 static void initVdwEwaldParameters(FILE *fp
, const t_inputrec
*ir
,
1825 interaction_const_t
*ic
)
1827 if (!EVDW_PME(ir
->vdwtype
))
1834 fprintf(fp
, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
1835 please_cite(fp
, "Essmann95a");
1837 ic
->ewaldcoeff_lj
= calc_ewaldcoeff_lj(ir
->rvdw
, ir
->ewald_rtol_lj
);
1840 fprintf(fp
, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
1841 1/ic
->ewaldcoeff_lj
);
1844 if (ic
->vdw_modifier
== eintmodPOTSHIFT
)
1846 real crc2
= gmx::square(ic
->ewaldcoeff_lj
*ic
->rvdw
);
1847 ic
->sh_lj_ewald
= (std::exp(-crc2
)*(1 + crc2
+ 0.5*crc2
*crc2
) - 1)/gmx::power6(ic
->rvdw
);
1851 ic
->sh_lj_ewald
= 0;
1855 gmx_bool
uses_simple_tables(int cutoff_scheme
,
1856 nonbonded_verlet_t
*nbv
,
1859 gmx_bool bUsesSimpleTables
= TRUE
;
1862 switch (cutoff_scheme
)
1865 bUsesSimpleTables
= TRUE
;
1868 assert(nullptr != nbv
);
1869 grp_index
= (group
< 0) ? 0 : (nbv
->ngrp
- 1);
1870 bUsesSimpleTables
= nbnxn_kernel_pairlist_simple(nbv
->grp
[grp_index
].kernel_type
);
1873 gmx_incons("unimplemented");
1875 return bUsesSimpleTables
;
1878 static void init_ewald_f_table(interaction_const_t
*ic
,
1883 /* Get the Ewald table spacing based on Coulomb and/or LJ
1884 * Ewald coefficients and rtol.
1886 ic
->tabq_scale
= ewald_spline3_table_scale(ic
);
1888 if (ic
->cutoff_scheme
== ecutsVERLET
)
1890 maxr
= ic
->rcoulomb
;
1894 maxr
= std::max(ic
->rcoulomb
, rtab
);
1896 ic
->tabq_size
= static_cast<int>(maxr
*ic
->tabq_scale
) + 2;
1898 sfree_aligned(ic
->tabq_coul_FDV0
);
1899 sfree_aligned(ic
->tabq_coul_F
);
1900 sfree_aligned(ic
->tabq_coul_V
);
1902 sfree_aligned(ic
->tabq_vdw_FDV0
);
1903 sfree_aligned(ic
->tabq_vdw_F
);
1904 sfree_aligned(ic
->tabq_vdw_V
);
1906 if (EEL_PME_EWALD(ic
->eeltype
))
1908 /* Create the original table data in FDV0 */
1909 snew_aligned(ic
->tabq_coul_FDV0
, ic
->tabq_size
*4, 32);
1910 snew_aligned(ic
->tabq_coul_F
, ic
->tabq_size
, 32);
1911 snew_aligned(ic
->tabq_coul_V
, ic
->tabq_size
, 32);
1912 table_spline3_fill_ewald_lr(ic
->tabq_coul_F
, ic
->tabq_coul_V
, ic
->tabq_coul_FDV0
,
1913 ic
->tabq_size
, 1/ic
->tabq_scale
, ic
->ewaldcoeff_q
, v_q_ewald_lr
);
1916 if (EVDW_PME(ic
->vdwtype
))
1918 snew_aligned(ic
->tabq_vdw_FDV0
, ic
->tabq_size
*4, 32);
1919 snew_aligned(ic
->tabq_vdw_F
, ic
->tabq_size
, 32);
1920 snew_aligned(ic
->tabq_vdw_V
, ic
->tabq_size
, 32);
1921 table_spline3_fill_ewald_lr(ic
->tabq_vdw_F
, ic
->tabq_vdw_V
, ic
->tabq_vdw_FDV0
,
1922 ic
->tabq_size
, 1/ic
->tabq_scale
, ic
->ewaldcoeff_lj
, v_lj_ewald_lr
);
1926 void init_interaction_const_tables(FILE *fp
,
1927 interaction_const_t
*ic
,
1930 if (EEL_PME_EWALD(ic
->eeltype
) || EVDW_PME(ic
->vdwtype
))
1932 init_ewald_f_table(ic
, rtab
);
1936 fprintf(fp
, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1937 1/ic
->tabq_scale
, ic
->tabq_size
);
1942 static void clear_force_switch_constants(shift_consts_t
*sc
)
1949 static void force_switch_constants(real p
,
1953 /* Here we determine the coefficient for shifting the force to zero
1954 * between distance rsw and the cut-off rc.
1955 * For a potential of r^-p, we have force p*r^-(p+1).
1956 * But to save flops we absorb p in the coefficient.
1958 * force/p = r^-(p+1) + c2*r^2 + c3*r^3
1959 * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
1961 sc
->c2
= ((p
+ 1)*rsw
- (p
+ 4)*rc
)/(pow(rc
, p
+ 2)*gmx::square(rc
- rsw
));
1962 sc
->c3
= -((p
+ 1)*rsw
- (p
+ 3)*rc
)/(pow(rc
, p
+ 2)*gmx::power3(rc
- rsw
));
1963 sc
->cpot
= -pow(rc
, -p
) + p
*sc
->c2
/3*gmx::power3(rc
- rsw
) + p
*sc
->c3
/4*gmx::power4(rc
- rsw
);
1966 static void potential_switch_constants(real rsw
, real rc
,
1967 switch_consts_t
*sc
)
1969 /* The switch function is 1 at rsw and 0 at rc.
1970 * The derivative and second derivate are zero at both ends.
1971 * rsw = max(r - r_switch, 0)
1972 * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
1973 * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
1974 * force = force*dsw - potential*sw
1977 sc
->c3
= -10/gmx::power3(rc
- rsw
);
1978 sc
->c4
= 15/gmx::power4(rc
- rsw
);
1979 sc
->c5
= -6/gmx::power5(rc
- rsw
);
1982 /*! \brief Construct interaction constants
1984 * This data is used (particularly) by search and force code for
1985 * short-range interactions. Many of these are constant for the whole
1986 * simulation; some are constant only after PME tuning completes.
1989 init_interaction_const(FILE *fp
,
1990 interaction_const_t
**interaction_const
,
1991 const t_inputrec
*ir
,
1992 const gmx_mtop_t
*mtop
,
1993 bool systemHasNetCharge
)
1995 interaction_const_t
*ic
;
1999 ic
->cutoff_scheme
= ir
->cutoff_scheme
;
2001 /* Just allocate something so we can free it */
2002 snew_aligned(ic
->tabq_coul_FDV0
, 16, 32);
2003 snew_aligned(ic
->tabq_coul_F
, 16, 32);
2004 snew_aligned(ic
->tabq_coul_V
, 16, 32);
2007 ic
->vdwtype
= ir
->vdwtype
;
2008 ic
->vdw_modifier
= ir
->vdw_modifier
;
2009 ic
->reppow
= mtop
->ffparams
.reppow
;
2010 ic
->rvdw
= cutoff_inf(ir
->rvdw
);
2011 ic
->rvdw_switch
= ir
->rvdw_switch
;
2012 ic
->ljpme_comb_rule
= ir
->ljpme_combination_rule
;
2013 ic
->useBuckingham
= (mtop
->ffparams
.functype
[0] == F_BHAM
);
2014 if (ic
->useBuckingham
)
2016 ic
->buckinghamBMax
= calcBuckinghamBMax(fp
, mtop
);
2019 initVdwEwaldParameters(fp
, ir
, ic
);
2021 clear_force_switch_constants(&ic
->dispersion_shift
);
2022 clear_force_switch_constants(&ic
->repulsion_shift
);
2024 switch (ic
->vdw_modifier
)
2026 case eintmodPOTSHIFT
:
2027 /* Only shift the potential, don't touch the force */
2028 ic
->dispersion_shift
.cpot
= -1.0/gmx::power6(ic
->rvdw
);
2029 ic
->repulsion_shift
.cpot
= -1.0/gmx::power12(ic
->rvdw
);
2031 case eintmodFORCESWITCH
:
2032 /* Switch the force, switch and shift the potential */
2033 force_switch_constants(6.0, ic
->rvdw_switch
, ic
->rvdw
,
2034 &ic
->dispersion_shift
);
2035 force_switch_constants(12.0, ic
->rvdw_switch
, ic
->rvdw
,
2036 &ic
->repulsion_shift
);
2038 case eintmodPOTSWITCH
:
2039 /* Switch the potential and force */
2040 potential_switch_constants(ic
->rvdw_switch
, ic
->rvdw
,
2044 case eintmodEXACTCUTOFF
:
2045 /* Nothing to do here */
2048 gmx_incons("unimplemented potential modifier");
2051 ic
->sh_invrc6
= -ic
->dispersion_shift
.cpot
;
2053 /* Electrostatics */
2054 ic
->eeltype
= ir
->coulombtype
;
2055 ic
->coulomb_modifier
= ir
->coulomb_modifier
;
2056 ic
->rcoulomb
= cutoff_inf(ir
->rcoulomb
);
2057 ic
->rcoulomb_switch
= ir
->rcoulomb_switch
;
2058 ic
->epsilon_r
= ir
->epsilon_r
;
2060 /* Set the Coulomb energy conversion factor */
2061 if (ic
->epsilon_r
!= 0)
2063 ic
->epsfac
= ONE_4PI_EPS0
/ic
->epsilon_r
;
2067 /* eps = 0 is infinite dieletric: no Coulomb interactions */
2071 /* Reaction-field */
2072 if (EEL_RF(ic
->eeltype
))
2074 ic
->epsilon_rf
= ir
->epsilon_rf
;
2075 /* Generalized reaction field parameters are updated every step */
2076 if (ic
->eeltype
!= eelGRF
)
2078 calc_rffac(fp
, ic
->eeltype
, ic
->epsilon_r
, ic
->epsilon_rf
,
2079 ic
->rcoulomb
, 0, 0, nullptr,
2080 &ic
->k_rf
, &ic
->c_rf
);
2083 if (ir
->cutoff_scheme
== ecutsGROUP
&& ic
->eeltype
== eelRF_ZERO
)
2085 /* grompp should have done this, but this scheme is obsolete */
2086 ic
->coulomb_modifier
= eintmodEXACTCUTOFF
;
2091 /* For plain cut-off we might use the reaction-field kernels */
2092 ic
->epsilon_rf
= ic
->epsilon_r
;
2094 if (ir
->coulomb_modifier
== eintmodPOTSHIFT
)
2096 ic
->c_rf
= 1/ic
->rcoulomb
;
2104 initCoulombEwaldParameters(fp
, ir
, systemHasNetCharge
, ic
);
2108 real dispersion_shift
;
2110 dispersion_shift
= ic
->dispersion_shift
.cpot
;
2111 if (EVDW_PME(ic
->vdwtype
))
2113 dispersion_shift
-= ic
->sh_lj_ewald
;
2115 fprintf(fp
, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
2116 ic
->repulsion_shift
.cpot
, dispersion_shift
);
2118 if (ic
->eeltype
== eelCUT
)
2120 fprintf(fp
, ", Coulomb %.e", -ic
->c_rf
);
2122 else if (EEL_PME(ic
->eeltype
))
2124 fprintf(fp
, ", Ewald %.3e", -ic
->sh_ewald
);
2129 *interaction_const
= ic
;
2133 done_interaction_const(interaction_const_t
*interaction_const
)
2135 sfree_aligned(interaction_const
->tabq_coul_FDV0
);
2136 sfree_aligned(interaction_const
->tabq_coul_F
);
2137 sfree_aligned(interaction_const
->tabq_coul_V
);
2138 sfree(interaction_const
);
2141 static void init_nb_verlet(const gmx::MDLogger
&mdlog
,
2142 nonbonded_verlet_t
**nb_verlet
,
2143 gmx_bool bFEP_NonBonded
,
2144 const t_inputrec
*ir
,
2145 const t_forcerec
*fr
,
2146 const t_commrec
*cr
,
2147 const gmx_hw_info_t
&hardwareInfo
,
2148 const gmx_device_info_t
*deviceInfo
,
2149 const gmx_mtop_t
*mtop
,
2152 nonbonded_verlet_t
*nbv
;
2155 nbnxn_alloc_t
*nb_alloc
;
2156 nbnxn_free_t
*nb_free
;
2158 nbv
= new nonbonded_verlet_t();
2160 nbv
->emulateGpu
= ((getenv("GMX_EMULATE_GPU") != nullptr) ? EmulateGpuNonbonded::Yes
: EmulateGpuNonbonded::No
);
2161 nbv
->bUseGPU
= deviceInfo
!= nullptr;
2163 GMX_RELEASE_ASSERT(!(nbv
->emulateGpu
== EmulateGpuNonbonded::Yes
&& nbv
->bUseGPU
), "When GPU emulation is active, there cannot be a GPU assignment");
2166 nbv
->min_ci_balanced
= 0;
2168 nbv
->ngrp
= (DOMAINDECOMP(cr
) ? 2 : 1);
2169 for (int i
= 0; i
< nbv
->ngrp
; i
++)
2171 nbv
->grp
[i
].nbl_lists
.nnbl
= 0;
2172 nbv
->grp
[i
].kernel_type
= nbnxnkNotSet
;
2174 if (i
== 0) /* local */
2176 pick_nbnxn_kernel(mdlog
, fr
->use_simd_kernels
, hardwareInfo
,
2177 nbv
->bUseGPU
, nbv
->emulateGpu
, ir
,
2178 &nbv
->grp
[i
].kernel_type
,
2179 &nbv
->grp
[i
].ewald_excl
,
2182 else /* non-local */
2184 /* Use the same kernel for local and non-local interactions */
2185 nbv
->grp
[i
].kernel_type
= nbv
->grp
[0].kernel_type
;
2186 nbv
->grp
[i
].ewald_excl
= nbv
->grp
[0].ewald_excl
;
2190 nbv
->listParams
= gmx::compat::make_unique
<NbnxnListParameters
>(ir
->rlist
);
2191 setupDynamicPairlistPruning(mdlog
, ir
, mtop
, box
, nbv
->grp
[0].kernel_type
, fr
->ic
,
2192 nbv
->listParams
.get());
2194 nbv
->nbs
= gmx::compat::make_unique
<nbnxn_search
>(DOMAINDECOMP(cr
) ? &cr
->dd
->nc
: nullptr,
2195 DOMAINDECOMP(cr
) ? domdec_zones(cr
->dd
) : nullptr,
2197 gmx_omp_nthreads_get(emntPairsearch
));
2199 gpu_set_host_malloc_and_free(nbv
->grp
[0].kernel_type
== nbnxnk8x8x8_GPU
,
2200 &nb_alloc
, &nb_free
);
2202 for (int i
= 0; i
< nbv
->ngrp
; i
++)
2204 nbnxn_init_pairlist_set(&nbv
->grp
[i
].nbl_lists
,
2205 nbnxn_kernel_pairlist_simple(nbv
->grp
[i
].kernel_type
),
2206 /* 8x8x8 "non-simple" lists are ATM always combined */
2207 !nbnxn_kernel_pairlist_simple(nbv
->grp
[i
].kernel_type
),
2211 int enbnxninitcombrule
;
2212 if (fr
->ic
->vdwtype
== evdwCUT
&&
2213 (fr
->ic
->vdw_modifier
== eintmodNONE
||
2214 fr
->ic
->vdw_modifier
== eintmodPOTSHIFT
) &&
2215 getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
2217 /* Plain LJ cut-off: we can optimize with combination rules */
2218 enbnxninitcombrule
= enbnxninitcombruleDETECT
;
2220 else if (fr
->ic
->vdwtype
== evdwPME
)
2222 /* LJ-PME: we need to use a combination rule for the grid */
2223 if (fr
->ljpme_combination_rule
== eljpmeGEOM
)
2225 enbnxninitcombrule
= enbnxninitcombruleGEOM
;
2229 enbnxninitcombrule
= enbnxninitcombruleLB
;
2234 /* We use a full combination matrix: no rule required */
2235 enbnxninitcombrule
= enbnxninitcombruleNONE
;
2239 int mimimumNumEnergyGroupNonbonded
= ir
->opts
.ngener
;
2240 if (ir
->opts
.ngener
- ir
->nwall
== 1)
2242 /* We have only one non-wall energy group, we do not need energy group
2243 * support in the non-bondeds kernels, since all non-bonded energy
2244 * contributions go to the first element of the energy group matrix.
2246 mimimumNumEnergyGroupNonbonded
= 1;
2248 bool bSimpleList
= nbnxn_kernel_pairlist_simple(nbv
->grp
[0].kernel_type
);
2249 nbnxn_atomdata_init(mdlog
,
2251 nbv
->grp
[0].kernel_type
,
2253 fr
->ntype
, fr
->nbfp
,
2254 mimimumNumEnergyGroupNonbonded
,
2255 bSimpleList
? gmx_omp_nthreads_get(emntNonbonded
) : 1,
2260 /* init the NxN GPU data; the last argument tells whether we'll have
2261 * both local and non-local NB calculation on GPU */
2262 nbnxn_gpu_init(&nbv
->gpu_nbv
,
2265 nbv
->listParams
.get(),
2270 if ((env
= getenv("GMX_NB_MIN_CI")) != nullptr)
2274 nbv
->min_ci_balanced
= strtol(env
, &end
, 10);
2275 if (!end
|| (*end
!= 0) || nbv
->min_ci_balanced
< 0)
2277 gmx_fatal(FARGS
, "Invalid value passed in GMX_NB_MIN_CI=%s, non-negative integer required", env
);
2282 fprintf(debug
, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
2283 nbv
->min_ci_balanced
);
2288 nbv
->min_ci_balanced
= nbnxn_gpu_min_ci_balanced(nbv
->gpu_nbv
);
2291 fprintf(debug
, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
2292 nbv
->min_ci_balanced
);
2301 gmx_bool
usingGpu(nonbonded_verlet_t
*nbv
)
2303 return nbv
!= nullptr && nbv
->bUseGPU
;
2306 void init_forcerec(FILE *fp
,
2307 const gmx::MDLogger
&mdlog
,
2310 const t_inputrec
*ir
,
2311 const gmx_mtop_t
*mtop
,
2312 const t_commrec
*cr
,
2316 gmx::ArrayRef
<const std::string
> tabbfnm
,
2317 const gmx_hw_info_t
&hardwareInfo
,
2318 const gmx_device_info_t
*deviceInfo
,
2319 const bool useGpuForBonded
,
2320 gmx_bool bNoSolvOpt
,
2323 int m
, negp_pp
, negptable
, egi
, egj
;
2328 gmx_bool bGenericKernelOnly
;
2329 gmx_bool needGroupSchemeTables
, bSomeNormalNbListsAreInUse
;
2330 gmx_bool bFEP_NonBonded
;
2331 int *nm_ind
, egp_flags
;
2333 /* By default we turn SIMD kernels on, but it might be turned off further down... */
2334 fr
->use_simd_kernels
= TRUE
;
2336 if (check_box(ir
->ePBC
, box
))
2338 gmx_fatal(FARGS
, "%s", check_box(ir
->ePBC
, box
));
2341 /* Test particle insertion ? */
2344 /* Set to the size of the molecule to be inserted (the last one) */
2345 /* Because of old style topologies, we have to use the last cg
2346 * instead of the last molecule type.
2348 cgs
= &mtop
->moltype
[mtop
->molblock
.back().type
].cgs
;
2349 fr
->n_tpi
= cgs
->index
[cgs
->nr
] - cgs
->index
[cgs
->nr
-1];
2350 gmx::RangePartitioning molecules
= gmx_mtop_molecules(*mtop
);
2351 if (fr
->n_tpi
!= molecules
.block(molecules
.numBlocks() - 1).size())
2353 gmx_fatal(FARGS
, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
2361 if (ir
->coulombtype
== eelRF_NEC_UNSUPPORTED
)
2363 gmx_fatal(FARGS
, "%s electrostatics is no longer supported",
2364 eel_names
[ir
->coulombtype
]);
2369 gmx_fatal(FARGS
, "AdResS simulations are no longer supported");
2371 if (ir
->useTwinRange
)
2373 gmx_fatal(FARGS
, "Twin-range simulations are no longer supported");
2375 /* Copy the user determined parameters */
2376 fr
->userint1
= ir
->userint1
;
2377 fr
->userint2
= ir
->userint2
;
2378 fr
->userint3
= ir
->userint3
;
2379 fr
->userint4
= ir
->userint4
;
2380 fr
->userreal1
= ir
->userreal1
;
2381 fr
->userreal2
= ir
->userreal2
;
2382 fr
->userreal3
= ir
->userreal3
;
2383 fr
->userreal4
= ir
->userreal4
;
2386 fr
->fc_stepsize
= ir
->fc_stepsize
;
2389 fr
->efep
= ir
->efep
;
2390 fr
->sc_alphavdw
= ir
->fepvals
->sc_alpha
;
2391 if (ir
->fepvals
->bScCoul
)
2393 fr
->sc_alphacoul
= ir
->fepvals
->sc_alpha
;
2394 fr
->sc_sigma6_min
= gmx::power6(ir
->fepvals
->sc_sigma_min
);
2398 fr
->sc_alphacoul
= 0;
2399 fr
->sc_sigma6_min
= 0; /* only needed when bScCoul is on */
2401 fr
->sc_power
= ir
->fepvals
->sc_power
;
2402 fr
->sc_r_power
= ir
->fepvals
->sc_r_power
;
2403 fr
->sc_sigma6_def
= gmx::power6(ir
->fepvals
->sc_sigma
);
2405 env
= getenv("GMX_SCSIGMA_MIN");
2409 sscanf(env
, "%20lf", &dbl
);
2410 fr
->sc_sigma6_min
= gmx::power6(dbl
);
2413 fprintf(fp
, "Setting the minimum soft core sigma to %g nm\n", dbl
);
2417 fr
->bNonbonded
= TRUE
;
2418 if (getenv("GMX_NO_NONBONDED") != nullptr)
2420 /* turn off non-bonded calculations */
2421 fr
->bNonbonded
= FALSE
;
2422 GMX_LOG(mdlog
.warning
).asParagraph().appendText(
2423 "Found environment variable GMX_NO_NONBONDED.\n"
2424 "Disabling nonbonded calculations.");
2427 bGenericKernelOnly
= FALSE
;
2429 /* We now check in the NS code whether a particular combination of interactions
2430 * can be used with water optimization, and disable it if that is not the case.
2433 if (getenv("GMX_NB_GENERIC") != nullptr)
2438 "Found environment variable GMX_NB_GENERIC.\n"
2439 "Disabling all interaction-specific nonbonded kernels, will only\n"
2440 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
2442 bGenericKernelOnly
= TRUE
;
2445 if (bGenericKernelOnly
)
2450 if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr) )
2452 fr
->use_simd_kernels
= FALSE
;
2456 "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
2457 "Disabling the usage of any SIMD-specific non-bonded & bonded kernel routines\n"
2458 "(e.g. SSE2/SSE4.1/AVX).\n\n");
2462 fr
->bBHAM
= (mtop
->ffparams
.functype
[0] == F_BHAM
);
2464 /* Check if we can/should do all-vs-all kernels */
2465 fr
->bAllvsAll
= can_use_allvsall(ir
, FALSE
, nullptr, nullptr);
2466 fr
->AllvsAll_work
= nullptr;
2468 /* All-vs-all kernels have not been implemented in 4.6 and later.
2469 * See Redmine #1249. */
2472 fr
->bAllvsAll
= FALSE
;
2476 "\nYour simulation settings would have triggered the efficient all-vs-all\n"
2477 "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
2478 "4.6 and 5.x. If performance is important, please use GROMACS 4.5.7\n"
2479 "or try cutoff-scheme = Verlet.\n\n");
2483 /* Neighbour searching stuff */
2484 fr
->cutoff_scheme
= ir
->cutoff_scheme
;
2485 fr
->bGrid
= (ir
->ns_type
== ensGRID
);
2486 fr
->ePBC
= ir
->ePBC
;
2488 if (fr
->cutoff_scheme
== ecutsGROUP
)
2490 const char *note
= "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
2491 "removed in a future release when 'verlet' supports all interaction forms.\n";
2495 fprintf(stderr
, "\n%s\n", note
);
2499 fprintf(fp
, "\n%s\n", note
);
2503 /* Determine if we will do PBC for distances in bonded interactions */
2504 if (fr
->ePBC
== epbcNONE
)
2506 fr
->bMolPBC
= FALSE
;
2510 if (!DOMAINDECOMP(cr
))
2514 bSHAKE
= (ir
->eConstrAlg
== econtSHAKE
&&
2515 (gmx_mtop_ftype_count(mtop
, F_CONSTR
) > 0 ||
2516 gmx_mtop_ftype_count(mtop
, F_CONSTRNC
) > 0));
2518 /* The group cut-off scheme and SHAKE assume charge groups
2519 * are whole, but not using molpbc is faster in most cases.
2520 * With intermolecular interactions we need PBC for calculating
2521 * distances between atoms in different molecules.
2523 if ((fr
->cutoff_scheme
== ecutsGROUP
|| bSHAKE
) &&
2524 !mtop
->bIntermolecularInteractions
)
2526 fr
->bMolPBC
= ir
->bPeriodicMols
;
2528 if (bSHAKE
&& fr
->bMolPBC
)
2530 gmx_fatal(FARGS
, "SHAKE is not supported with periodic molecules");
2535 /* Not making molecules whole is faster in most cases,
2536 * but With orientation restraints we need whole molecules.
2538 fr
->bMolPBC
= (fcd
->orires
.nr
== 0);
2540 if (getenv("GMX_USE_GRAPH") != nullptr)
2542 fr
->bMolPBC
= FALSE
;
2545 GMX_LOG(mdlog
.warning
).asParagraph().appendText("GMX_USE_GRAPH is set, using the graph for bonded interactions");
2548 if (mtop
->bIntermolecularInteractions
)
2550 GMX_LOG(mdlog
.warning
).asParagraph().appendText("WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!");
2554 GMX_RELEASE_ASSERT(fr
->bMolPBC
|| !mtop
->bIntermolecularInteractions
, "We need to use PBC within molecules with inter-molecular interactions");
2556 if (bSHAKE
&& fr
->bMolPBC
)
2558 gmx_fatal(FARGS
, "SHAKE is not properly supported with intermolecular interactions. For short simulations where linked molecules remain in the same periodic image, the environment variable GMX_USE_GRAPH can be used to override this check.\n");
2564 fr
->bMolPBC
= dd_bonded_molpbc(cr
->dd
, fr
->ePBC
);
2568 fr
->rc_scaling
= ir
->refcoord_scaling
;
2569 copy_rvec(ir
->posres_com
, fr
->posres_com
);
2570 copy_rvec(ir
->posres_comB
, fr
->posres_comB
);
2571 fr
->rlist
= cutoff_inf(ir
->rlist
);
2572 fr
->ljpme_combination_rule
= ir
->ljpme_combination_rule
;
2574 /* This now calculates sum for q and c6*/
2575 bool systemHasNetCharge
= set_chargesum(fp
, fr
, mtop
);
2577 /* fr->ic is used both by verlet and group kernels (to some extent) now */
2578 init_interaction_const(fp
, &fr
->ic
, ir
, mtop
, systemHasNetCharge
);
2579 init_interaction_const_tables(fp
, fr
->ic
, ir
->rlist
+ ir
->tabext
);
2581 const interaction_const_t
*ic
= fr
->ic
;
2583 /* TODO: Replace this Ewald table or move it into interaction_const_t */
2584 if (ir
->coulombtype
== eelEWALD
)
2586 init_ewald_tab(&(fr
->ewald_table
), ir
, fp
);
2589 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2590 switch (ic
->eeltype
)
2593 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_COULOMB
;
2598 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_REACTIONFIELD
;
2602 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_REACTIONFIELD
;
2603 GMX_RELEASE_ASSERT(ic
->coulomb_modifier
== eintmodEXACTCUTOFF
, "With the group scheme RF-zero needs the exact cut-off modifier");
2612 case eelPMEUSERSWITCH
:
2613 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_CUBICSPLINETABLE
;
2619 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_EWALD
;
2623 gmx_fatal(FARGS
, "Unsupported electrostatic interaction: %s", eel_names
[ic
->eeltype
]);
2625 fr
->nbkernel_elec_modifier
= ic
->coulomb_modifier
;
2627 /* Vdw: Translate from mdp settings to kernel format */
2628 switch (ic
->vdwtype
)
2633 fr
->nbkernel_vdw_interaction
= GMX_NBKERNEL_VDW_BUCKINGHAM
;
2637 fr
->nbkernel_vdw_interaction
= GMX_NBKERNEL_VDW_LENNARDJONES
;
2641 fr
->nbkernel_vdw_interaction
= GMX_NBKERNEL_VDW_LJEWALD
;
2647 case evdwENCADSHIFT
:
2648 fr
->nbkernel_vdw_interaction
= GMX_NBKERNEL_VDW_CUBICSPLINETABLE
;
2652 gmx_fatal(FARGS
, "Unsupported vdw interaction: %s", evdw_names
[ic
->vdwtype
]);
2654 fr
->nbkernel_vdw_modifier
= ic
->vdw_modifier
;
2656 if (ir
->cutoff_scheme
== ecutsGROUP
)
2658 fr
->bvdwtab
= ((ic
->vdwtype
!= evdwCUT
|| !gmx_within_tol(ic
->reppow
, 12.0, 10*GMX_DOUBLE_EPS
))
2659 && !EVDW_PME(ic
->vdwtype
));
2660 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2661 fr
->bcoultab
= !(ic
->eeltype
== eelCUT
||
2662 ic
->eeltype
== eelEWALD
||
2663 ic
->eeltype
== eelPME
||
2664 ic
->eeltype
== eelP3M_AD
||
2665 ic
->eeltype
== eelRF
||
2666 ic
->eeltype
== eelRF_ZERO
);
2668 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2669 * going to be faster to tabulate the interaction than calling the generic kernel.
2670 * However, if generic kernels have been requested we keep things analytically.
2672 if (fr
->nbkernel_elec_modifier
== eintmodPOTSWITCH
&&
2673 fr
->nbkernel_vdw_modifier
== eintmodPOTSWITCH
&&
2674 !bGenericKernelOnly
)
2676 if ((ic
->rcoulomb_switch
!= ic
->rvdw_switch
) || (ic
->rcoulomb
!= ic
->rvdw
))
2678 fr
->bcoultab
= TRUE
;
2679 /* Once we tabulate electrostatics, we can use the switch function for LJ,
2680 * which would otherwise need two tables.
2684 else if ((fr
->nbkernel_elec_modifier
== eintmodPOTSHIFT
&& fr
->nbkernel_vdw_modifier
== eintmodPOTSHIFT
) ||
2685 ((fr
->nbkernel_elec_interaction
== GMX_NBKERNEL_ELEC_REACTIONFIELD
&&
2686 fr
->nbkernel_elec_modifier
== eintmodEXACTCUTOFF
&&
2687 (fr
->nbkernel_vdw_modifier
== eintmodPOTSWITCH
|| fr
->nbkernel_vdw_modifier
== eintmodPOTSHIFT
))))
2689 if ((ic
->rcoulomb
!= ic
->rvdw
) && (!bGenericKernelOnly
))
2691 fr
->bcoultab
= TRUE
;
2695 if (fr
->nbkernel_elec_modifier
== eintmodFORCESWITCH
)
2697 fr
->bcoultab
= TRUE
;
2699 if (fr
->nbkernel_vdw_modifier
== eintmodFORCESWITCH
)
2704 if (getenv("GMX_REQUIRE_TABLES"))
2707 fr
->bcoultab
= TRUE
;
2712 fprintf(fp
, "Table routines are used for coulomb: %s\n",
2713 gmx::boolToString(fr
->bcoultab
));
2714 fprintf(fp
, "Table routines are used for vdw: %s\n",
2715 gmx::boolToString(fr
->bvdwtab
));
2720 fr
->nbkernel_vdw_interaction
= GMX_NBKERNEL_VDW_CUBICSPLINETABLE
;
2721 fr
->nbkernel_vdw_modifier
= eintmodNONE
;
2725 fr
->nbkernel_elec_interaction
= GMX_NBKERNEL_ELEC_CUBICSPLINETABLE
;
2726 fr
->nbkernel_elec_modifier
= eintmodNONE
;
2730 if (ir
->cutoff_scheme
== ecutsVERLET
)
2732 if (!gmx_within_tol(ic
->reppow
, 12.0, 10*GMX_DOUBLE_EPS
))
2734 gmx_fatal(FARGS
, "Cut-off scheme %s only supports LJ repulsion power 12", ecutscheme_names
[ir
->cutoff_scheme
]);
2736 /* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
2737 * while mdrun does not (and never did) support this.
2739 if (EEL_USER(fr
->ic
->eeltype
))
2741 gmx_fatal(FARGS
, "Combination of %s and cutoff scheme %s is not supported",
2742 eel_names
[ir
->coulombtype
], ecutscheme_names
[ir
->cutoff_scheme
]);
2745 fr
->bvdwtab
= FALSE
;
2746 fr
->bcoultab
= FALSE
;
2749 /* 1-4 interaction electrostatics */
2750 fr
->fudgeQQ
= mtop
->ffparams
.fudgeQQ
;
2752 /* Parameters for generalized RF */
2756 if (ic
->eeltype
== eelGRF
)
2758 init_generalized_rf(fp
, mtop
, ir
, fr
);
2761 fr
->haveDirectVirialContributions
=
2762 (EEL_FULL(ic
->eeltype
) || EVDW_PME(ic
->vdwtype
) ||
2763 fr
->forceProviders
->hasForceProvider() ||
2764 gmx_mtop_ftype_count(mtop
, F_POSRES
) > 0 ||
2765 gmx_mtop_ftype_count(mtop
, F_FBPOSRES
) > 0 ||
2771 if (fr
->haveDirectVirialContributions
)
2773 fr
->forceBufferForDirectVirialContributions
= new std::vector
<gmx::RVec
>;
2776 if (fr
->cutoff_scheme
== ecutsGROUP
&&
2777 ncg_mtop(mtop
) > fr
->cg_nalloc
&& !DOMAINDECOMP(cr
))
2779 /* Count the total number of charge groups */
2780 fr
->cg_nalloc
= ncg_mtop(mtop
);
2781 srenew(fr
->cg_cm
, fr
->cg_nalloc
);
2783 if (fr
->shift_vec
== nullptr)
2785 snew(fr
->shift_vec
, SHIFTS
);
2788 if (fr
->fshift
== nullptr)
2790 snew(fr
->fshift
, SHIFTS
);
2793 if (fr
->nbfp
== nullptr)
2795 fr
->ntype
= mtop
->ffparams
.atnr
;
2796 fr
->nbfp
= mk_nbfp(&mtop
->ffparams
, fr
->bBHAM
);
2797 if (EVDW_PME(ic
->vdwtype
))
2799 fr
->ljpme_c6grid
= make_ljpme_c6grid(&mtop
->ffparams
, fr
);
2803 /* Copy the energy group exclusions */
2804 fr
->egp_flags
= ir
->opts
.egp_flags
;
2806 /* Van der Waals stuff */
2807 if ((ic
->vdwtype
!= evdwCUT
) && (ic
->vdwtype
!= evdwUSER
) && !fr
->bBHAM
)
2809 if (ic
->rvdw_switch
>= ic
->rvdw
)
2811 gmx_fatal(FARGS
, "rvdw_switch (%f) must be < rvdw (%f)",
2812 ic
->rvdw_switch
, ic
->rvdw
);
2816 fprintf(fp
, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2817 (ic
->eeltype
== eelSWITCH
) ? "switched" : "shifted",
2818 ic
->rvdw_switch
, ic
->rvdw
);
2822 if (fr
->bBHAM
&& EVDW_PME(ic
->vdwtype
))
2824 gmx_fatal(FARGS
, "LJ PME not supported with Buckingham");
2827 if (fr
->bBHAM
&& (ic
->vdwtype
== evdwSHIFT
|| ic
->vdwtype
== evdwSWITCH
))
2829 gmx_fatal(FARGS
, "Switch/shift interaction not supported with Buckingham");
2832 if (fr
->bBHAM
&& fr
->cutoff_scheme
== ecutsVERLET
)
2834 gmx_fatal(FARGS
, "Verlet cutoff-scheme is not supported with Buckingham");
2837 if (fp
&& fr
->cutoff_scheme
== ecutsGROUP
)
2839 fprintf(fp
, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2840 fr
->rlist
, ic
->rcoulomb
, fr
->bBHAM
? "BHAM" : "LJ", ic
->rvdw
);
2843 fr
->eDispCorr
= ir
->eDispCorr
;
2844 fr
->numAtomsForDispersionCorrection
= mtop
->natoms
;
2845 if (ir
->eDispCorr
!= edispcNO
)
2847 set_avcsixtwelve(fp
, fr
, mtop
);
2850 if (ir
->implicit_solvent
)
2852 gmx_fatal(FARGS
, "Implict solvation is no longer supported.");
2855 /* Construct tables for the group scheme. A little unnecessary to
2856 * make both vdw and coul tables sometimes, but what the
2857 * heck. Note that both cutoff schemes construct Ewald tables in
2858 * init_interaction_const_tables. */
2859 needGroupSchemeTables
= (ir
->cutoff_scheme
== ecutsGROUP
&&
2860 (fr
->bcoultab
|| fr
->bvdwtab
));
2862 negp_pp
= ir
->opts
.ngener
- ir
->nwall
;
2864 if (!needGroupSchemeTables
)
2866 bSomeNormalNbListsAreInUse
= TRUE
;
2871 bSomeNormalNbListsAreInUse
= FALSE
;
2872 for (egi
= 0; egi
< negp_pp
; egi
++)
2874 for (egj
= egi
; egj
< negp_pp
; egj
++)
2876 egp_flags
= ir
->opts
.egp_flags
[GID(egi
, egj
, ir
->opts
.ngener
)];
2877 if (!(egp_flags
& EGP_EXCL
))
2879 if (egp_flags
& EGP_TABLE
)
2885 bSomeNormalNbListsAreInUse
= TRUE
;
2890 if (bSomeNormalNbListsAreInUse
)
2892 fr
->nnblists
= negptable
+ 1;
2896 fr
->nnblists
= negptable
;
2898 if (fr
->nnblists
> 1)
2900 snew(fr
->gid2nblists
, ir
->opts
.ngener
*ir
->opts
.ngener
);
2904 snew(fr
->nblists
, fr
->nnblists
);
2906 /* This code automatically gives table length tabext without cut-off's,
2907 * in that case grompp should already have checked that we do not need
2908 * normal tables and we only generate tables for 1-4 interactions.
2910 rtab
= ir
->rlist
+ ir
->tabext
;
2912 if (needGroupSchemeTables
)
2914 /* make tables for ordinary interactions */
2915 if (bSomeNormalNbListsAreInUse
)
2917 make_nbf_tables(fp
, ic
, rtab
, tabfn
, nullptr, nullptr, &fr
->nblists
[0]);
2926 /* Read the special tables for certain energy group pairs */
2927 nm_ind
= mtop
->groups
.grps
[egcENER
].nm_ind
;
2928 for (egi
= 0; egi
< negp_pp
; egi
++)
2930 for (egj
= egi
; egj
< negp_pp
; egj
++)
2932 egp_flags
= ir
->opts
.egp_flags
[GID(egi
, egj
, ir
->opts
.ngener
)];
2933 if ((egp_flags
& EGP_TABLE
) && !(egp_flags
& EGP_EXCL
))
2935 if (fr
->nnblists
> 1)
2937 fr
->gid2nblists
[GID(egi
, egj
, ir
->opts
.ngener
)] = m
;
2939 /* Read the table file with the two energy groups names appended */
2940 make_nbf_tables(fp
, ic
, rtab
, tabfn
,
2941 *mtop
->groups
.grpname
[nm_ind
[egi
]],
2942 *mtop
->groups
.grpname
[nm_ind
[egj
]],
2946 else if (fr
->nnblists
> 1)
2948 fr
->gid2nblists
[GID(egi
, egj
, ir
->opts
.ngener
)] = 0;
2955 /* Tables might not be used for the potential modifier
2956 * interactions per se, but we still need them to evaluate
2957 * switch/shift dispersion corrections in this case. */
2958 if (fr
->eDispCorr
!= edispcNO
)
2960 fr
->dispersionCorrectionTable
= makeDispersionCorrectionTable(fp
, ic
, rtab
, tabfn
);
2963 /* We want to use unmodified tables for 1-4 coulombic
2964 * interactions, so we must in general have an extra set of
2966 if (gmx_mtop_ftype_count(mtop
, F_LJ14
) > 0 ||
2967 gmx_mtop_ftype_count(mtop
, F_LJC14_Q
) > 0 ||
2968 gmx_mtop_ftype_count(mtop
, F_LJC_PAIRS_NB
) > 0)
2970 fr
->pairsTable
= make_tables(fp
, ic
, tabpfn
, rtab
,
2971 GMX_MAKETABLES_14ONLY
);
2975 fr
->nwall
= ir
->nwall
;
2976 if (ir
->nwall
&& ir
->wall_type
== ewtTABLE
)
2978 make_wall_tables(fp
, ir
, tabfn
, &mtop
->groups
, fr
);
2981 if (fcd
&& !tabbfnm
.empty())
2983 // Need to catch std::bad_alloc
2984 // TODO Don't need to catch this here, when merging with master branch
2987 fcd
->bondtab
= make_bonded_tables(fp
,
2988 F_TABBONDS
, F_TABBONDSNC
,
2989 mtop
, tabbfnm
, "b");
2990 fcd
->angletab
= make_bonded_tables(fp
,
2992 mtop
, tabbfnm
, "a");
2993 fcd
->dihtab
= make_bonded_tables(fp
,
2995 mtop
, tabbfnm
, "d");
2997 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
3003 fprintf(debug
, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
3007 // QM/MM initialization if requested
3008 fr
->bQMMM
= ir
->bQMMM
;
3011 // Initialize QM/MM if supported
3014 GMX_LOG(mdlog
.info
).asParagraph().
3015 appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
3016 "version. Please get in touch with the developers if you find the support useful, "
3017 "as help is needed if the functionality is to continue to be available.");
3018 fr
->qr
= mk_QMMMrec();
3019 init_QMMMrec(cr
, mtop
, ir
, fr
);
3023 gmx_incons("QM/MM was requested, but is only available when GROMACS "
3024 "is configured with QM/MM support");
3028 /* Set all the static charge group info */
3029 fr
->cginfo_mb
= init_cginfo_mb(fp
, mtop
, fr
, bNoSolvOpt
,
3031 &fr
->bExcl_IntraCGAll_InterCGNone
);
3032 if (DOMAINDECOMP(cr
))
3034 fr
->cginfo
= nullptr;
3038 fr
->cginfo
= cginfo_expand(mtop
->molblock
.size(), fr
->cginfo_mb
);
3041 if (!DOMAINDECOMP(cr
))
3043 forcerec_set_ranges(fr
, ncg_mtop(mtop
), ncg_mtop(mtop
),
3044 mtop
->natoms
, mtop
->natoms
, mtop
->natoms
);
3047 fr
->print_force
= print_force
;
3050 /* coarse load balancing vars */
3055 /* Initialize neighbor search */
3057 init_ns(fp
, cr
, fr
->ns
, fr
, mtop
);
3059 if (thisRankHasDuty(cr
, DUTY_PP
))
3061 gmx_nonbonded_setup(fr
, bGenericKernelOnly
);
3064 /* Initialize the thread working data for bonded interactions */
3065 init_bonded_threading(fp
, mtop
->groups
.grps
[egcENER
].nr
,
3066 &fr
->bondedThreading
);
3068 fr
->nthread_ewc
= gmx_omp_nthreads_get(emntBonded
);
3069 snew(fr
->ewc_t
, fr
->nthread_ewc
);
3071 if (fr
->cutoff_scheme
== ecutsVERLET
)
3073 // We checked the cut-offs in grompp, but double-check here.
3074 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
3075 if (EEL_PME_EWALD(ir
->coulombtype
) && ir
->vdwtype
== eelCUT
)
3077 GMX_RELEASE_ASSERT(ir
->rcoulomb
>= ir
->rvdw
, "With Verlet lists and PME we should have rcoulomb>=rvdw");
3081 GMX_RELEASE_ASSERT(ir
->rcoulomb
== ir
->rvdw
, "With Verlet lists and no PME rcoulomb and rvdw should be identical");
3084 init_nb_verlet(mdlog
, &fr
->nbv
, bFEP_NonBonded
, ir
, fr
,
3085 cr
, hardwareInfo
, deviceInfo
,
3088 if (useGpuForBonded
)
3090 auto stream
= DOMAINDECOMP(cr
) ?
3091 nbnxn_gpu_get_command_stream(fr
->nbv
->gpu_nbv
, eintNonlocal
) :
3092 nbnxn_gpu_get_command_stream(fr
->nbv
->gpu_nbv
, eintLocal
);
3093 // TODO the heap allocation is only needed while
3094 // t_forcerec lacks a constructor.
3095 fr
->gpuBonded
= new gmx::GpuBonded(mtop
->ffparams
,
3102 /* Here we switch from using mdlog, which prints the newline before
3103 * the paragraph, to our old fprintf logging, which prints the newline
3104 * after the paragraph, so we should add a newline here.
3109 if (ir
->eDispCorr
!= edispcNO
)
3111 calc_enervirdiff(fp
, ir
->eDispCorr
, fr
);
3115 /* Frees GPU memory and sets a tMPI node barrier.
3117 * Note that this function needs to be called even if GPUs are not used
3118 * in this run because the PME ranks have no knowledge of whether GPUs
3119 * are used or not, but all ranks need to enter the barrier below.
3120 * \todo Remove physical node barrier from this function after making sure
3121 * that it's not needed anymore (with a shared GPU run).
3123 void free_gpu_resources(t_forcerec
*fr
,
3124 const gmx::PhysicalNodeCommunicator
&physicalNodeCommunicator
)
3126 bool isPPrankUsingGPU
= (fr
!= nullptr) && (fr
->nbv
!= nullptr) && fr
->nbv
->bUseGPU
;
3128 /* stop the GPU profiler (only CUDA) */
3131 if (isPPrankUsingGPU
)
3133 /* free nbnxn data in GPU memory */
3134 nbnxn_gpu_free(fr
->nbv
->gpu_nbv
);
3135 delete fr
->gpuBonded
;
3136 fr
->gpuBonded
= nullptr;
3139 /* With tMPI we need to wait for all ranks to finish deallocation before
3140 * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
3143 * This is not a concern in OpenCL where we use one context per rank which
3144 * is freed in nbnxn_gpu_free().
3146 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
3147 * but it is easier and more futureproof to call it on the whole node.
3151 physicalNodeCommunicator
.barrier();
3155 void done_forcerec(t_forcerec
*fr
, int numMolBlocks
, int numEnergyGroups
)
3159 // PME-only ranks don't have a forcerec
3162 // cginfo is dynamically allocated if no domain decomposition
3163 if (fr
->cginfo
!= nullptr)
3167 done_cginfo_mb(fr
->cginfo_mb
, numMolBlocks
);
3169 done_interaction_const(fr
->ic
);
3170 sfree(fr
->shift_vec
);
3173 done_ns(fr
->ns
, numEnergyGroups
);
3175 tear_down_bonded_threading(fr
->bondedThreading
);
3176 GMX_RELEASE_ASSERT(fr
->gpuBonded
== nullptr, "Should have been deleted earlier, when used");
3177 fr
->bondedThreading
= nullptr;