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45 #include "gromacs/compat/make_unique.h"
46 #include "gromacs/gpu_utils/hostallocator.h"
47 #include "gromacs/math/functions.h"
48 #include "gromacs/mdlib/gmx_omp_nthreads.h"
49 #include "gromacs/mdlib/qmmm.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/md_enums.h"
52 #include "gromacs/topology/mtop_lookup.h"
53 #include "gromacs/topology/mtop_util.h"
54 #include "gromacs/topology/topology.h"
55 #include "gromacs/utility/exceptions.h"
56 #include "gromacs/utility/smalloc.h"
58 #define ALMOST_ZERO 1e-30
64 : mdatoms_(nullptr), chargeA_()
70 if (mdatoms_
== nullptr)
74 sfree(mdatoms_
->massA
);
75 sfree(mdatoms_
->massB
);
76 sfree(mdatoms_
->massT
);
77 gmx::AlignedAllocationPolicy::free(mdatoms_
->invmass
);
78 sfree(mdatoms_
->invMassPerDim
);
79 sfree(mdatoms_
->typeA
);
80 sfree(mdatoms_
->chargeB
);
81 sfree(mdatoms_
->typeB
);
82 sfree(mdatoms_
->sqrt_c6A
);
83 sfree(mdatoms_
->sigmaA
);
84 sfree(mdatoms_
->sigma3A
);
85 sfree(mdatoms_
->sqrt_c6B
);
86 sfree(mdatoms_
->sigmaB
);
87 sfree(mdatoms_
->sigma3B
);
88 sfree(mdatoms_
->ptype
);
90 sfree(mdatoms_
->cENER
);
91 sfree(mdatoms_
->cACC
);
92 sfree(mdatoms_
->cFREEZE
);
93 sfree(mdatoms_
->cVCM
);
94 sfree(mdatoms_
->cORF
);
95 sfree(mdatoms_
->bPerturbed
);
101 void MDAtoms::resize(int newSize
)
103 chargeA_
.resize(newSize
);
104 mdatoms_
->chargeA
= chargeA_
.data();
107 void MDAtoms::reserve(int newCapacity
)
109 chargeA_
.reserve(newCapacity
);
110 mdatoms_
->chargeA
= chargeA_
.data();
113 std::unique_ptr
<MDAtoms
>
114 makeMDAtoms(FILE *fp
, const gmx_mtop_t
&mtop
, const t_inputrec
&ir
,
117 auto mdAtoms
= compat::make_unique
<MDAtoms
>();
118 // GPU transfers want to use the pinning mode.
119 changePinningPolicy(&mdAtoms
->chargeA_
, useGpuForPme
? PinningPolicy::CanBePinned
: PinningPolicy::CannotBePinned
);
122 mdAtoms
->mdatoms_
.reset(md
);
124 md
->nenergrp
= mtop
.groups
.grps
[egcENER
].nr
;
125 md
->bVCMgrps
= FALSE
;
126 for (int i
= 0; i
< mtop
.natoms
; i
++)
128 if (ggrpnr(&mtop
.groups
, egcVCM
, i
) > 0)
134 /* Determine the total system mass and perturbed atom counts */
135 double totalMassA
= 0.0;
136 double totalMassB
= 0.0;
138 md
->haveVsites
= FALSE
;
139 gmx_mtop_atomloop_block_t aloop
= gmx_mtop_atomloop_block_init(&mtop
);
142 while (gmx_mtop_atomloop_block_next(aloop
, &atom
, &nmol
))
144 totalMassA
+= nmol
*atom
->m
;
145 totalMassB
+= nmol
*atom
->mB
;
147 if (atom
->ptype
== eptVSite
)
149 md
->haveVsites
= TRUE
;
152 if (ir
.efep
!= efepNO
&& PERTURBED(*atom
))
155 if (atom
->mB
!= atom
->m
)
157 md
->nMassPerturbed
+= nmol
;
159 if (atom
->qB
!= atom
->q
)
161 md
->nChargePerturbed
+= nmol
;
163 if (atom
->typeB
!= atom
->type
)
165 md
->nTypePerturbed
+= nmol
;
170 md
->tmassA
= totalMassA
;
171 md
->tmassB
= totalMassB
;
173 if (ir
.efep
!= efepNO
&& fp
)
176 "There are %d atoms and %d charges for free energy perturbation\n",
177 md
->nPerturbed
, md
->nChargePerturbed
);
180 md
->havePartiallyFrozenAtoms
= FALSE
;
181 for (int g
= 0; g
< ir
.opts
.ngfrz
; g
++)
183 for (int d
= YY
; d
< DIM
; d
++)
185 if (ir
.opts
.nFreeze
[d
] != ir
.opts
.nFreeze
[XX
])
187 md
->havePartiallyFrozenAtoms
= TRUE
;
192 md
->bOrires
= gmx_mtop_ftype_count(&mtop
, F_ORIRES
);
199 void atoms2md(const gmx_mtop_t
*mtop
, const t_inputrec
*ir
,
200 int nindex
, const int *index
,
202 gmx::MDAtoms
*mdAtoms
)
205 const t_grpopts
*opts
;
206 const gmx_groups_t
*groups
;
207 int nthreads gmx_unused
;
209 bLJPME
= EVDW_PME(ir
->vdwtype
);
213 groups
= &mtop
->groups
;
215 auto md
= mdAtoms
->mdatoms();
216 /* nindex>=0 indicates DD where we use an index */
223 md
->nr
= mtop
->natoms
;
226 if (md
->nr
> md
->nalloc
)
228 md
->nalloc
= over_alloc_dd(md
->nr
);
230 if (md
->nMassPerturbed
)
232 srenew(md
->massA
, md
->nalloc
);
233 srenew(md
->massB
, md
->nalloc
);
235 srenew(md
->massT
, md
->nalloc
);
236 /* The SIMD version of the integrator needs this aligned and padded.
237 * The padding needs to be with zeros, which we set later below.
239 gmx::AlignedAllocationPolicy::free(md
->invmass
);
240 md
->invmass
= new(gmx::AlignedAllocationPolicy::malloc((md
->nalloc
+ GMX_REAL_MAX_SIMD_WIDTH
)*sizeof(*md
->invmass
)))real
;
241 srenew(md
->invMassPerDim
, md
->nalloc
);
242 // TODO eventually we will have vectors and just resize
243 // everything, but for now the semantics of md->nalloc being
244 // the capacity are preserved by keeping vectors within
245 // mdAtoms having the same properties as the other arrays.
246 mdAtoms
->reserve(md
->nalloc
);
247 mdAtoms
->resize(md
->nr
);
248 srenew(md
->typeA
, md
->nalloc
);
251 srenew(md
->chargeB
, md
->nalloc
);
252 srenew(md
->typeB
, md
->nalloc
);
256 srenew(md
->sqrt_c6A
, md
->nalloc
);
257 srenew(md
->sigmaA
, md
->nalloc
);
258 srenew(md
->sigma3A
, md
->nalloc
);
261 srenew(md
->sqrt_c6B
, md
->nalloc
);
262 srenew(md
->sigmaB
, md
->nalloc
);
263 srenew(md
->sigma3B
, md
->nalloc
);
266 srenew(md
->ptype
, md
->nalloc
);
269 srenew(md
->cTC
, md
->nalloc
);
270 /* We always copy cTC with domain decomposition */
272 srenew(md
->cENER
, md
->nalloc
);
275 srenew(md
->cACC
, md
->nalloc
);
279 opts
->nFreeze
[0][XX
] || opts
->nFreeze
[0][YY
] || opts
->nFreeze
[0][ZZ
]))
281 srenew(md
->cFREEZE
, md
->nalloc
);
285 srenew(md
->cVCM
, md
->nalloc
);
289 srenew(md
->cORF
, md
->nalloc
);
293 srenew(md
->bPerturbed
, md
->nalloc
);
296 /* Note that these user t_mdatoms array pointers are NULL
297 * when there is only one group present.
298 * Therefore, when adding code, the user should use something like:
299 * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
301 if (mtop
->groups
.grpnr
[egcUser1
] != nullptr)
303 srenew(md
->cU1
, md
->nalloc
);
305 if (mtop
->groups
.grpnr
[egcUser2
] != nullptr)
307 srenew(md
->cU2
, md
->nalloc
);
312 srenew(md
->bQM
, md
->nalloc
);
318 // cppcheck-suppress unreadVariable
319 nthreads
= gmx_omp_nthreads_get(emntDefault
);
320 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
321 for (int i
= 0; i
< md
->nr
; i
++)
329 if (index
== nullptr)
337 const t_atom
&atom
= mtopGetAtomParameters(mtop
, ag
, &molb
);
341 md
->cFREEZE
[i
] = ggrpnr(groups
, egcFREEZE
, ag
);
343 if (EI_ENERGY_MINIMIZATION(ir
->eI
))
345 /* Displacement is proportional to F, masses used for constraints */
349 else if (ir
->eI
== eiBD
)
351 /* With BD the physical masses are irrelevant.
352 * To keep the code simple we use most of the normal MD code path
353 * for BD. Thus for constraining the masses should be proportional
354 * to the friction coefficient. We set the absolute value such that
355 * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
356 * Then if we set the (meaningless) velocity to v=dx/dt, we get the
357 * correct kinetic energy and temperature using the usual code path.
358 * Thus with BD v*dt will give the displacement and the reported
359 * temperature can signal bad integration (too large time step).
363 mA
= 0.5*ir
->bd_fric
*ir
->delta_t
;
364 mB
= 0.5*ir
->bd_fric
*ir
->delta_t
;
368 /* The friction coefficient is mass/tau_t */
369 fac
= ir
->delta_t
/opts
->tau_t
[md
->cTC
? groups
->grpnr
[egcTC
][ag
] : 0];
371 mB
= 0.5*atom
.mB
*fac
;
379 if (md
->nMassPerturbed
)
389 md
->invMassPerDim
[i
][XX
] = 0;
390 md
->invMassPerDim
[i
][YY
] = 0;
391 md
->invMassPerDim
[i
][ZZ
] = 0;
393 else if (md
->cFREEZE
)
396 if (opts
->nFreeze
[g
][XX
] && opts
->nFreeze
[g
][YY
] && opts
->nFreeze
[g
][ZZ
])
398 /* Set the mass of completely frozen particles to ALMOST_ZERO
399 * iso 0 to avoid div by zero in lincs or shake.
401 md
->invmass
[i
] = ALMOST_ZERO
;
405 /* Note: Partially frozen particles use the normal invmass.
406 * If such particles are constrained, the frozen dimensions
407 * should not be updated with the constrained coordinates.
409 md
->invmass
[i
] = 1.0/mA
;
411 for (int d
= 0; d
< DIM
; d
++)
413 md
->invMassPerDim
[i
][d
] = (opts
->nFreeze
[g
][d
] ? 0 : 1.0/mA
);
418 md
->invmass
[i
] = 1.0/mA
;
419 for (int d
= 0; d
< DIM
; d
++)
421 md
->invMassPerDim
[i
][d
] = 1.0/mA
;
425 md
->chargeA
[i
] = atom
.q
;
426 md
->typeA
[i
] = atom
.type
;
429 c6
= mtop
->ffparams
.iparams
[atom
.type
*(mtop
->ffparams
.atnr
+1)].lj
.c6
;
430 c12
= mtop
->ffparams
.iparams
[atom
.type
*(mtop
->ffparams
.atnr
+1)].lj
.c12
;
431 md
->sqrt_c6A
[i
] = sqrt(c6
);
432 if (c6
== 0.0 || c12
== 0)
438 md
->sigmaA
[i
] = gmx::sixthroot(c12
/c6
);
440 md
->sigma3A
[i
] = 1/(md
->sigmaA
[i
]*md
->sigmaA
[i
]*md
->sigmaA
[i
]);
444 md
->bPerturbed
[i
] = PERTURBED(atom
);
445 md
->chargeB
[i
] = atom
.qB
;
446 md
->typeB
[i
] = atom
.typeB
;
449 c6
= mtop
->ffparams
.iparams
[atom
.typeB
*(mtop
->ffparams
.atnr
+1)].lj
.c6
;
450 c12
= mtop
->ffparams
.iparams
[atom
.typeB
*(mtop
->ffparams
.atnr
+1)].lj
.c12
;
451 md
->sqrt_c6B
[i
] = sqrt(c6
);
452 if (c6
== 0.0 || c12
== 0)
458 md
->sigmaB
[i
] = gmx::sixthroot(c12
/c6
);
460 md
->sigma3B
[i
] = 1/(md
->sigmaB
[i
]*md
->sigmaB
[i
]*md
->sigmaB
[i
]);
463 md
->ptype
[i
] = atom
.ptype
;
466 md
->cTC
[i
] = groups
->grpnr
[egcTC
][ag
];
468 md
->cENER
[i
] = ggrpnr(groups
, egcENER
, ag
);
471 md
->cACC
[i
] = groups
->grpnr
[egcACC
][ag
];
475 md
->cVCM
[i
] = groups
->grpnr
[egcVCM
][ag
];
479 md
->cORF
[i
] = ggrpnr(groups
, egcORFIT
, ag
);
484 md
->cU1
[i
] = groups
->grpnr
[egcUser1
][ag
];
488 md
->cU2
[i
] = groups
->grpnr
[egcUser2
][ag
];
493 if (groups
->grpnr
[egcQMMM
] == nullptr ||
494 groups
->grpnr
[egcQMMM
][ag
] < groups
->grps
[egcQMMM
].nr
-1)
504 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
509 /* Pad invmass with 0 so a SIMD MD update does not change v and x */
510 for (int i
= md
->nr
; i
< md
->nr
+ GMX_REAL_MAX_SIMD_WIDTH
; i
++)
517 /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
518 * For free-energy runs, these should be updated using update_mdatoms().
520 md
->tmass
= md
->tmassA
;
524 void update_mdatoms(t_mdatoms
*md
, real lambda
)
526 if (md
->nMassPerturbed
&& lambda
!= md
->lambda
)
528 real L1
= 1 - lambda
;
530 /* Update masses of perturbed atoms for the change in lambda */
531 // cppcheck-suppress unreadVariable
532 int gmx_unused nthreads
= gmx_omp_nthreads_get(emntDefault
);
533 #pragma omp parallel for num_threads(nthreads) schedule(static)
534 for (int i
= 0; i
< md
->nr
; i
++)
536 if (md
->bPerturbed
[i
])
538 md
->massT
[i
] = L1
*md
->massA
[i
] + lambda
*md
->massB
[i
];
539 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
540 * and their invmass does not depend on lambda.
542 if (md
->invmass
[i
] > 1.1*ALMOST_ZERO
)
544 md
->invmass
[i
] = 1.0/md
->massT
[i
];
545 for (int d
= 0; d
< DIM
; d
++)
547 if (md
->invMassPerDim
[i
][d
] > 1.1*ALMOST_ZERO
)
549 md
->invMassPerDim
[i
][d
] = md
->invmass
[i
];
556 /* Update the system mass for the change in lambda */
557 md
->tmass
= L1
*md
->tmassA
+ lambda
*md
->tmassB
;