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40 * \brief This file defines the integrator for test particle insertion
42 * \author Berk Hess <hess@kth.se>
43 * \ingroup module_mdrun
56 #include "gromacs/commandline/filenm.h"
57 #include "gromacs/domdec/dlbtiming.h"
58 #include "gromacs/domdec/domdec.h"
59 #include "gromacs/ewald/pme.h"
60 #include "gromacs/fileio/confio.h"
61 #include "gromacs/fileio/trxio.h"
62 #include "gromacs/fileio/xvgr.h"
63 #include "gromacs/gmxlib/conformation_utilities.h"
64 #include "gromacs/gmxlib/network.h"
65 #include "gromacs/gmxlib/nrnb.h"
66 #include "gromacs/math/units.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/mdlib/constr.h"
69 #include "gromacs/mdlib/dispersioncorrection.h"
70 #include "gromacs/mdlib/energyoutput.h"
71 #include "gromacs/mdlib/force.h"
72 #include "gromacs/mdlib/force_flags.h"
73 #include "gromacs/mdlib/gmx_omp_nthreads.h"
74 #include "gromacs/mdlib/mdatoms.h"
75 #include "gromacs/mdlib/tgroup.h"
76 #include "gromacs/mdlib/update.h"
77 #include "gromacs/mdlib/vsite.h"
78 #include "gromacs/mdrunutility/printtime.h"
79 #include "gromacs/mdtypes/commrec.h"
80 #include "gromacs/mdtypes/forcerec.h"
81 #include "gromacs/mdtypes/group.h"
82 #include "gromacs/mdtypes/inputrec.h"
83 #include "gromacs/mdtypes/md_enums.h"
84 #include "gromacs/mdtypes/mdrunoptions.h"
85 #include "gromacs/mdtypes/state.h"
86 #include "gromacs/nbnxm/nbnxm.h"
87 #include "gromacs/pbcutil/pbc.h"
88 #include "gromacs/random/threefry.h"
89 #include "gromacs/random/uniformrealdistribution.h"
90 #include "gromacs/timing/wallcycle.h"
91 #include "gromacs/timing/walltime_accounting.h"
92 #include "gromacs/topology/mtop_util.h"
93 #include "gromacs/trajectory/trajectoryframe.h"
94 #include "gromacs/utility/cstringutil.h"
95 #include "gromacs/utility/fatalerror.h"
96 #include "gromacs/utility/gmxassert.h"
97 #include "gromacs/utility/logger.h"
98 #include "gromacs/utility/smalloc.h"
100 #include "legacysimulator.h"
102 //! Global max algorithm
103 static void global_max(t_commrec
* cr
, int* n
)
107 snew(sum
, cr
->nnodes
);
108 sum
[cr
->nodeid
] = *n
;
109 gmx_sumi(cr
->nnodes
, sum
, cr
);
110 for (i
= 0; i
< cr
->nnodes
; i
++)
112 *n
= std::max(*n
, sum
[i
]);
118 //! Reallocate arrays.
119 static void realloc_bins(double** bin
, int* nbin
, int nbin_new
)
123 if (nbin_new
!= *nbin
)
125 srenew(*bin
, nbin_new
);
126 for (i
= *nbin
; i
< nbin_new
; i
++)
134 //! Computes and returns the RF exclusion energy for the last molecule starting at \p beginAtom
135 static real
reactionFieldExclusionCorrection(gmx::ArrayRef
<const gmx::RVec
> x
,
136 const t_mdatoms
& mdatoms
,
137 const interaction_const_t
& ic
,
142 for (int i
= beginAtom
; i
< mdatoms
.homenr
; i
++)
144 const real qi
= mdatoms
.chargeA
[i
];
145 energy
-= 0.5 * qi
* qi
* ic
.c_rf
;
147 for (int j
= i
+ 1; j
< mdatoms
.homenr
; j
++)
149 const real qj
= mdatoms
.chargeA
[j
];
150 const real rsq
= distance2(x
[i
], x
[j
]);
151 energy
+= qi
* qj
* (ic
.k_rf
* rsq
- ic
.c_rf
);
155 return ic
.epsfac
* energy
;
161 // TODO: Convert to use the nbnxm kernels by putting the system and the teset molecule on two separate search grids
162 void LegacySimulator::do_tpi()
164 GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault
) == 1, "TPI does not support OpenMP");
167 PaddedHostVector
<gmx::RVec
> f
{};
168 real lambda
, t
, temp
, beta
, drmax
, epot
;
169 double embU
, sum_embU
, *sum_UgembU
, V
, V_all
, VembU_all
;
172 gmx_bool bDispCorr
, bCharge
, bRFExcl
, bNotLastFrame
, bStateChanged
, bNS
;
173 tensor force_vir
, shake_vir
, vir
, pres
;
174 int a_tp0
, a_tp1
, ngid
, gid_tp
, nener
, e
;
176 rvec mu_tot
, x_init
, dx
;
178 int64_t frame_step_prev
, frame_step
;
179 int64_t nsteps
, stepblocksize
= 0, step
;
182 FILE* fp_tpi
= nullptr;
183 char * ptr
, *dump_pdb
, **leg
, str
[STRLEN
], str2
[STRLEN
];
184 double dbl
, dump_ener
;
186 int nat_cavity
= 0, d
;
187 real
* mass_cavity
= nullptr, mass_tot
;
189 double invbinw
, *bin
, refvolshift
, logV
, bUlogV
;
190 gmx_bool bEnergyOutOfBounds
;
191 const char* tpid_leg
[2] = { "direct", "reweighted" };
192 auto mdatoms
= mdAtoms
->mdatoms();
194 GMX_UNUSED_VALUE(outputProvider
);
199 "Note that it is planned to change the command gmx mdrun -tpi "
200 "(and -tpic) to make the functionality available in a different "
201 "form in a future version of GROMACS, e.g. gmx test-particle-insertion.");
203 /* Since there is no upper limit to the insertion energies,
204 * we need to set an upper limit for the distribution output.
206 real bU_bin_limit
= 50;
207 real bU_logV_bin_limit
= bU_bin_limit
+ 10;
211 gmx_mtop_generate_local_top(*top_global
, &top
, inputrec
->efep
!= efepNO
);
213 SimulationGroups
* groups
= &top_global
->groups
;
215 bCavity
= (inputrec
->eI
== eiTPIC
);
218 ptr
= getenv("GMX_TPIC_MASSES");
225 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
226 * The center of mass of the last atoms is then used for TPIC.
229 while (sscanf(ptr
, "%20lf%n", &dbl
, &i
) > 0)
231 srenew(mass_cavity
, nat_cavity
+ 1);
232 mass_cavity
[nat_cavity
] = dbl
;
233 fprintf(fplog
, "mass[%d] = %f\n", nat_cavity
+ 1, mass_cavity
[nat_cavity
]);
239 gmx_fatal(FARGS
, "Found %d masses in GMX_TPIC_MASSES", nat_cavity
);
245 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
246 state_global->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
247 /* We never need full pbc for TPI */
249 /* Determine the temperature for the Boltzmann weighting */
250 temp
= inputrec
->opts
.ref_t
[0];
253 for (i
= 1; (i
< inputrec
->opts
.ngtc
); i
++)
255 if (inputrec
->opts
.ref_t
[i
] != temp
)
258 "\nWARNING: The temperatures of the different temperature coupling groups "
259 "are not identical\n\n");
261 "\nWARNING: The temperatures of the different temperature coupling groups "
262 "are not identical\n\n");
265 fprintf(fplog
, "\n The temperature for test particle insertion is %.3f K\n\n", temp
);
267 beta
= 1.0 / (BOLTZ
* temp
);
269 /* Number of insertions per frame */
270 nsteps
= inputrec
->nsteps
;
272 /* Use the same neighborlist with more insertions points
273 * in a sphere of radius drmax around the initial point
275 /* This should be a proper mdp parameter */
276 drmax
= inputrec
->rtpi
;
278 /* An environment variable can be set to dump all configurations
279 * to pdb with an insertion energy <= this value.
281 dump_pdb
= getenv("GMX_TPI_DUMP");
285 sscanf(dump_pdb
, "%20lf", &dump_ener
);
288 atoms2md(top_global
, inputrec
, -1, nullptr, top_global
->natoms
, mdAtoms
);
289 update_mdatoms(mdatoms
, inputrec
->fepvals
->init_lambda
);
291 f
.resizeWithPadding(top_global
->natoms
);
293 /* Print to log file */
294 walltime_accounting_start_time(walltime_accounting
);
295 wallcycle_start(wcycle
, ewcRUN
);
296 print_start(fplog
, cr
, walltime_accounting
, "Test Particle Insertion");
298 /* The last charge group is the group to be inserted */
299 const t_atoms
& atomsToInsert
= top_global
->moltype
[top_global
->molblock
.back().type
].atoms
;
300 a_tp0
= top_global
->natoms
- atomsToInsert
.nr
;
301 a_tp1
= top_global
->natoms
;
304 fprintf(debug
, "TPI atoms %d-%d\n", a_tp0
, a_tp1
);
307 auto x
= makeArrayRef(state_global
->x
);
309 if (EEL_PME(fr
->ic
->eeltype
))
311 gmx_pme_reinit_atoms(fr
->pmedata
, a_tp0
, nullptr);
314 /* With reacion-field we have distance dependent potentials
315 * between excluded atoms, we need to add these separately
316 * for the inserted molecule.
318 real rfExclusionEnergy
= 0;
319 if (EEL_RF(fr
->ic
->eeltype
))
321 rfExclusionEnergy
= reactionFieldExclusionCorrection(x
, *mdatoms
, *fr
->ic
, a_tp0
);
324 fprintf(debug
, "RF exclusion correction for inserted molecule: %f kJ/mol\n", rfExclusionEnergy
);
328 snew(x_mol
, a_tp1
- a_tp0
);
330 bDispCorr
= (inputrec
->eDispCorr
!= edispcNO
);
332 for (i
= a_tp0
; i
< a_tp1
; i
++)
334 /* Copy the coordinates of the molecule to be insterted */
335 copy_rvec(x
[i
], x_mol
[i
- a_tp0
]);
336 /* Check if we need to print electrostatic energies */
337 bCharge
|= (mdatoms
->chargeA
[i
] != 0
338 || ((mdatoms
->chargeB
!= nullptr) && mdatoms
->chargeB
[i
] != 0));
340 bRFExcl
= (bCharge
&& EEL_RF(fr
->ic
->eeltype
));
342 // Calculate the center of geometry of the molecule to insert
343 rvec cog
= { 0, 0, 0 };
344 for (int a
= a_tp0
; a
< a_tp1
; a
++)
348 svmul(1.0_real
/ (a_tp1
- a_tp0
), cog
, cog
);
350 for (int a
= a_tp0
; a
< a_tp1
; a
++)
352 molRadius
= std::max(molRadius
, distance2(x
[a
], cog
));
354 molRadius
= std::sqrt(molRadius
);
356 const real maxCutoff
= std::max(inputrec
->rvdw
, inputrec
->rcoulomb
);
359 if (norm(cog
) > 0.5 * maxCutoff
&& fplog
)
361 fprintf(fplog
, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
362 fprintf(stderr
, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
367 /* Center the molecule to be inserted at zero */
368 for (i
= 0; i
< a_tp1
- a_tp0
; i
++)
370 rvec_dec(x_mol
[i
], cog
);
376 fprintf(fplog
, "\nWill insert %d atoms %s partial charges\n", a_tp1
- a_tp0
,
377 bCharge
? "with" : "without");
379 fprintf(fplog
, "\nWill insert %" PRId64
" times in each frame of %s\n", nsteps
,
380 opt2fn("-rerun", nfile
, fnm
));
385 if (inputrec
->nstlist
> 1)
388 /* With the same pair list we insert in a sphere of radius rtpi in different orientations */
389 if (drmax
== 0 && a_tp1
- a_tp0
== 1)
392 "Re-using the neighborlist %d times for insertions of a single atom in a "
393 "sphere of radius %f does not make sense",
394 inputrec
->nstlist
, drmax
);
399 "Will use the same neighborlist for %d insertions in a sphere of radius "
401 inputrec
->nstlist
, drmax
);
410 "Will insert randomly in a sphere of radius %f around the center of the "
416 /* With the same pair list we insert in a sphere of radius rtpi
417 * in different orientations. We generate the pairlist with all
418 * inserted atoms located in the center of the sphere, so we need
419 * a buffer of size of the sphere and molecule radius.
421 inputrec
->rlist
= maxCutoff
+ 2 * inputrec
->rtpi
+ 2 * molRadius
;
422 fr
->rlist
= inputrec
->rlist
;
423 fr
->nbv
->changePairlistRadii(inputrec
->rlist
, inputrec
->rlist
);
425 ngid
= groups
->groups
[SimulationAtomGroupType::EnergyOutput
].size();
426 gid_tp
= GET_CGINFO_GID(fr
->cginfo
[a_tp0
]);
427 for (int a
= a_tp0
+ 1; a
< a_tp1
; a
++)
429 if (GET_CGINFO_GID(fr
->cginfo
[a
]) != gid_tp
)
432 "NOTE: Atoms in the molecule to insert belong to different energy groups.\n"
433 " Only contributions to the group of the first atom will be reported.\n");
449 if (EEL_FULL(fr
->ic
->eeltype
))
454 snew(sum_UgembU
, nener
);
456 /* Copy the random seed set by the user */
457 seed
= inputrec
->ld_seed
;
459 gmx::ThreeFry2x64
<16> rng(
460 seed
, gmx::RandomDomain::TestParticleInsertion
); // 16 bits internal counter => 2^16 * 2 = 131072 values per stream
461 gmx::UniformRealDistribution
<real
> dist
;
465 fp_tpi
= xvgropen(opt2fn("-tpi", nfile
, fnm
), "TPI energies", "Time (ps)",
466 "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv
);
467 xvgr_subtitle(fp_tpi
, "f. are averages over one frame", oenv
);
468 snew(leg
, 4 + nener
);
470 sprintf(str
, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
471 leg
[e
++] = gmx_strdup(str
);
472 sprintf(str
, "f. -kT log<e\\S-\\betaU\\N>");
473 leg
[e
++] = gmx_strdup(str
);
474 sprintf(str
, "f. <e\\S-\\betaU\\N>");
475 leg
[e
++] = gmx_strdup(str
);
476 sprintf(str
, "f. V");
477 leg
[e
++] = gmx_strdup(str
);
478 sprintf(str
, "f. <Ue\\S-\\betaU\\N>");
479 leg
[e
++] = gmx_strdup(str
);
480 for (i
= 0; i
< ngid
; i
++)
482 sprintf(str
, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
483 *(groups
->groupNames
[groups
->groups
[SimulationAtomGroupType::EnergyOutput
][i
]]));
484 leg
[e
++] = gmx_strdup(str
);
488 sprintf(str
, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
489 leg
[e
++] = gmx_strdup(str
);
493 for (i
= 0; i
< ngid
; i
++)
495 sprintf(str
, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
496 *(groups
->groupNames
[groups
->groups
[SimulationAtomGroupType::EnergyOutput
][i
]]));
497 leg
[e
++] = gmx_strdup(str
);
501 sprintf(str
, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
502 leg
[e
++] = gmx_strdup(str
);
504 if (EEL_FULL(fr
->ic
->eeltype
))
506 sprintf(str
, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
507 leg
[e
++] = gmx_strdup(str
);
510 xvgr_legend(fp_tpi
, 4 + nener
, leg
, oenv
);
511 for (i
= 0; i
< 4 + nener
; i
++)
525 /* Avoid frame step numbers <= -1 */
526 frame_step_prev
= -1;
528 bNotLastFrame
= read_first_frame(oenv
, &status
, opt2fn("-rerun", nfile
, fnm
), &rerun_fr
, TRX_NEED_X
);
531 if (rerun_fr
.natoms
- (bCavity
? nat_cavity
: 0) != mdatoms
->nr
- (a_tp1
- a_tp0
))
534 "Number of atoms in trajectory (%d)%s "
535 "is not equal the number in the run input file (%d) "
536 "minus the number of atoms to insert (%d)\n",
537 rerun_fr
.natoms
, bCavity
? " minus one" : "", mdatoms
->nr
, a_tp1
- a_tp0
);
540 refvolshift
= log(det(rerun_fr
.box
));
542 switch (inputrec
->eI
)
544 case eiTPI
: stepblocksize
= inputrec
->nstlist
; break;
545 case eiTPIC
: stepblocksize
= 1; break;
546 default: gmx_fatal(FARGS
, "Unknown integrator %s", ei_names
[inputrec
->eI
]);
549 while (bNotLastFrame
)
551 frame_step
= rerun_fr
.step
;
552 if (frame_step
<= frame_step_prev
)
554 /* We don't have step number in the trajectory file,
555 * or we have constant or decreasing step numbers.
556 * Ensure we have increasing step numbers, since we use
557 * the step numbers as a counter for random numbers.
559 frame_step
= frame_step_prev
+ 1;
561 frame_step_prev
= frame_step
;
563 lambda
= rerun_fr
.lambda
;
567 for (e
= 0; e
< nener
; e
++)
572 /* Copy the coordinates from the input trajectory */
573 auto x
= makeArrayRef(state_global
->x
);
574 for (i
= 0; i
< rerun_fr
.natoms
; i
++)
576 copy_rvec(rerun_fr
.x
[i
], x
[i
]);
578 copy_mat(rerun_fr
.box
, state_global
->box
);
579 const matrix
& box
= state_global
->box
;
584 bStateChanged
= TRUE
;
587 put_atoms_in_box(fr
->ePBC
, box
, x
);
589 /* Put all atoms except for the inserted ones on the grid */
590 rvec vzero
= { 0, 0, 0 };
591 rvec boxDiagonal
= { box
[XX
][XX
], box
[YY
][YY
], box
[ZZ
][ZZ
] };
592 nbnxn_put_on_grid(fr
->nbv
.get(), box
, 0, vzero
, boxDiagonal
, nullptr, { 0, a_tp0
}, -1,
593 fr
->cginfo
, x
, 0, nullptr);
595 step
= cr
->nodeid
* stepblocksize
;
596 while (step
< nsteps
)
598 /* Restart random engine using the frame and insertion step
600 * Note that we need to draw several random values per iteration,
601 * but by using the internal subcounter functionality of ThreeFry2x64
602 * we can draw 131072 unique 64-bit values before exhausting
603 * the stream. This is a huge margin, and if something still goes
604 * wrong you will get an exception when the stream is exhausted.
606 rng
.restart(frame_step
, step
);
607 dist
.reset(); // erase any memory in the distribution
611 /* Random insertion in the whole volume */
612 bNS
= (step
% inputrec
->nstlist
== 0);
615 /* Generate a random position in the box */
616 for (d
= 0; d
< DIM
; d
++)
618 x_init
[d
] = dist(rng
) * state_global
->box
[d
][d
];
624 /* Random insertion around a cavity location
625 * given by the last coordinate of the trajectory.
631 /* Copy the location of the cavity */
632 copy_rvec(rerun_fr
.x
[rerun_fr
.natoms
- 1], x_init
);
636 /* Determine the center of mass of the last molecule */
639 for (i
= 0; i
< nat_cavity
; i
++)
641 for (d
= 0; d
< DIM
; d
++)
643 x_init
[d
] += mass_cavity
[i
]
644 * rerun_fr
.x
[rerun_fr
.natoms
- nat_cavity
+ i
][d
];
646 mass_tot
+= mass_cavity
[i
];
648 for (d
= 0; d
< DIM
; d
++)
650 x_init
[d
] /= mass_tot
;
658 for (int a
= a_tp0
; a
< a_tp1
; a
++)
663 /* Put the inserted molecule on it's own search grid */
664 nbnxn_put_on_grid(fr
->nbv
.get(), box
, 1, x_init
, x_init
, nullptr, { a_tp0
, a_tp1
},
665 -1, fr
->cginfo
, x
, 0, nullptr);
667 /* TODO: Avoid updating all atoms at every bNS step */
668 fr
->nbv
->setAtomProperties(*mdatoms
, fr
->cginfo
);
670 fr
->nbv
->constructPairlist(InteractionLocality::Local
, top
.excls
, step
, nrnb
);
675 /* Add random displacement uniformly distributed in a sphere
676 * of radius rtpi. We don't need to do this is we generate
677 * a new center location every step.
680 if (bCavity
|| inputrec
->nstlist
> 1)
682 /* Generate coordinates within |dx|=drmax of x_init */
685 for (d
= 0; d
< DIM
; d
++)
687 dx
[d
] = (2 * dist(rng
) - 1) * drmax
;
689 } while (norm2(dx
) > drmax
* drmax
);
690 rvec_add(x_init
, dx
, x_tp
);
694 copy_rvec(x_init
, x_tp
);
697 if (a_tp1
- a_tp0
== 1)
699 /* Insert a single atom, just copy the insertion location */
700 copy_rvec(x_tp
, x
[a_tp0
]);
704 /* Copy the coordinates from the top file */
705 for (i
= a_tp0
; i
< a_tp1
; i
++)
707 copy_rvec(x_mol
[i
- a_tp0
], x
[i
]);
709 /* Rotate the molecule randomly */
710 real angleX
= 2 * M_PI
* dist(rng
);
711 real angleY
= 2 * M_PI
* dist(rng
);
712 real angleZ
= 2 * M_PI
* dist(rng
);
713 rotate_conf(a_tp1
- a_tp0
, state_global
->x
.rvec_array() + a_tp0
, nullptr, angleX
,
715 /* Shift to the insertion location */
716 for (i
= a_tp0
; i
< a_tp1
; i
++)
718 rvec_inc(x
[i
], x_tp
);
722 /* Note: NonLocal refers to the inserted molecule */
723 fr
->nbv
->convertCoordinates(AtomLocality::NonLocal
, false, x
);
725 /* Clear some matrix variables */
726 clear_mat(force_vir
);
727 clear_mat(shake_vir
);
731 /* Calc energy (no forces) on new positions.
732 * Since we only need the intermolecular energy
733 * and the RF exclusion terms of the inserted molecule occur
734 * within a single charge group we can pass NULL for the graph.
735 * This also avoids shifts that would move charge groups
737 /* Make do_force do a single node force calculation */
740 // TPI might place a particle so close that the potential
741 // is infinite. Since this is intended to happen, we
742 // temporarily suppress any exceptions that the processor
743 // might raise, then restore the old behaviour.
744 std::fenv_t floatingPointEnvironment
;
745 std::feholdexcept(&floatingPointEnvironment
);
746 do_force(fplog
, cr
, ms
, inputrec
, nullptr, nullptr, imdSession
, pull_work
, step
, nrnb
,
747 wcycle
, &top
, state_global
->box
, state_global
->x
.arrayRefWithPadding(),
748 &state_global
->hist
, f
.arrayRefWithPadding(), force_vir
, mdatoms
, enerd
, fcd
,
749 state_global
->lambda
, nullptr, fr
, runScheduleWork
, nullptr, mu_tot
, t
, nullptr,
750 GMX_FORCE_NONBONDED
| GMX_FORCE_ENERGY
| (bStateChanged
? GMX_FORCE_STATECHANGED
: 0),
751 DDBalanceRegionHandler(nullptr));
752 std::feclearexcept(FE_DIVBYZERO
| FE_INVALID
| FE_OVERFLOW
);
753 std::feupdateenv(&floatingPointEnvironment
);
756 bStateChanged
= FALSE
;
758 if (fr
->dispersionCorrection
)
760 /* Calculate long range corrections to pressure and energy */
761 const DispersionCorrection::Correction correction
=
762 fr
->dispersionCorrection
->calculate(state_global
->box
, lambda
);
763 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
764 enerd
->term
[F_DISPCORR
] = correction
.energy
;
765 enerd
->term
[F_EPOT
] += correction
.energy
;
766 enerd
->term
[F_PRES
] += correction
.pressure
;
767 enerd
->term
[F_DVDL
] += correction
.dvdl
;
771 enerd
->term
[F_DISPCORR
] = 0;
773 if (EEL_RF(fr
->ic
->eeltype
))
775 enerd
->term
[F_EPOT
] += rfExclusionEnergy
;
778 epot
= enerd
->term
[F_EPOT
];
779 bEnergyOutOfBounds
= FALSE
;
781 /* If the compiler doesn't optimize this check away
782 * we catch the NAN energies.
783 * The epot>GMX_REAL_MAX check catches inf values,
784 * which should nicely result in embU=0 through the exp below,
785 * but it does not hurt to check anyhow.
787 /* Non-bonded Interaction usually diverge at r=0.
788 * With tabulated interaction functions the first few entries
789 * should be capped in a consistent fashion between
790 * repulsion, dispersion and Coulomb to avoid accidental
791 * negative values in the total energy.
792 * The table generation code in tables.c does this.
793 * With user tbales the user should take care of this.
795 if (epot
!= epot
|| epot
> GMX_REAL_MAX
)
797 bEnergyOutOfBounds
= TRUE
;
799 if (bEnergyOutOfBounds
)
804 "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t
,
805 static_cast<int>(step
), epot
);
811 // Exponent argument is fine in SP range, but output can be in DP range
812 embU
= exp(static_cast<double>(-beta
* epot
));
814 /* Determine the weighted energy contributions of each energy group */
816 sum_UgembU
[e
++] += epot
* embU
;
819 for (i
= 0; i
< ngid
; i
++)
821 sum_UgembU
[e
++] += enerd
->grpp
.ener
[egBHAMSR
][GID(i
, gid_tp
, ngid
)] * embU
;
826 for (i
= 0; i
< ngid
; i
++)
828 sum_UgembU
[e
++] += enerd
->grpp
.ener
[egLJSR
][GID(i
, gid_tp
, ngid
)] * embU
;
833 sum_UgembU
[e
++] += enerd
->term
[F_DISPCORR
] * embU
;
837 for (i
= 0; i
< ngid
; i
++)
839 sum_UgembU
[e
++] += enerd
->grpp
.ener
[egCOULSR
][GID(i
, gid_tp
, ngid
)] * embU
;
843 sum_UgembU
[e
++] += rfExclusionEnergy
* embU
;
845 if (EEL_FULL(fr
->ic
->eeltype
))
847 sum_UgembU
[e
++] += enerd
->term
[F_COUL_RECIP
] * embU
;
852 if (embU
== 0 || beta
* epot
> bU_bin_limit
)
858 i
= gmx::roundToInt((bU_logV_bin_limit
- (beta
* epot
- logV
+ refvolshift
)) * invbinw
);
865 realloc_bins(&bin
, &nbin
, i
+ 10);
872 fprintf(debug
, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n", static_cast<int>(step
),
873 epot
, x_tp
[XX
], x_tp
[YY
], x_tp
[ZZ
]);
876 if (dump_pdb
&& epot
<= dump_ener
)
878 sprintf(str
, "t%g_step%d.pdb", t
, static_cast<int>(step
));
879 sprintf(str2
, "t: %f step %d ener: %f", t
, static_cast<int>(step
), epot
);
880 write_sto_conf_mtop(str
, str2
, top_global
, state_global
->x
.rvec_array(),
881 state_global
->v
.rvec_array(), inputrec
->ePBC
, state_global
->box
);
885 if ((step
/ stepblocksize
) % cr
->nnodes
!= cr
->nodeid
)
887 /* Skip all steps assigned to the other MPI ranks */
888 step
+= (cr
->nnodes
- 1) * stepblocksize
;
894 /* When running in parallel sum the energies over the processes */
895 gmx_sumd(1, &sum_embU
, cr
);
896 gmx_sumd(nener
, sum_UgembU
, cr
);
901 VembU_all
+= V
* sum_embU
/ nsteps
;
905 if (mdrunOptions
.verbose
|| frame
% 10 == 0 || frame
< 10)
907 fprintf(stderr
, "mu %10.3e <mu> %10.3e\n", -log(sum_embU
/ nsteps
) / beta
,
908 -log(VembU_all
/ V_all
) / beta
);
911 fprintf(fp_tpi
, "%10.3f %12.5e %12.5e %12.5e %12.5e", t
,
912 VembU_all
== 0 ? 20 / beta
: -log(VembU_all
/ V_all
) / beta
,
913 sum_embU
== 0 ? 20 / beta
: -log(sum_embU
/ nsteps
) / beta
, sum_embU
/ nsteps
, V
);
914 for (e
= 0; e
< nener
; e
++)
916 fprintf(fp_tpi
, " %12.5e", sum_UgembU
[e
] / nsteps
);
918 fprintf(fp_tpi
, "\n");
922 bNotLastFrame
= read_next_frame(oenv
, status
, &rerun_fr
);
923 } /* End of the loop */
924 walltime_accounting_end_time(walltime_accounting
);
928 if (fp_tpi
!= nullptr)
933 if (fplog
!= nullptr)
935 fprintf(fplog
, "\n");
936 fprintf(fplog
, " <V> = %12.5e nm^3\n", V_all
/ frame
);
937 const double mu
= -log(VembU_all
/ V_all
) / beta
;
938 fprintf(fplog
, " <mu> = %12.5e kJ/mol\n", mu
);
940 if (!std::isfinite(mu
))
943 "\nThe computed chemical potential is not finite - consider increasing the "
944 "number of steps and/or the number of frames to insert into.\n");
948 /* Write the Boltzmann factor histogram */
951 /* When running in parallel sum the bins over the processes */
954 realloc_bins(&bin
, &nbin
, i
);
955 gmx_sumd(nbin
, bin
, cr
);
959 fp_tpi
= xvgropen(opt2fn("-tpid", nfile
, fnm
), "TPI energy distribution",
960 "\\betaU - log(V/<V>)", "count", oenv
);
961 sprintf(str
, "number \\betaU > %g: %9.3e", bU_bin_limit
, bin
[0]);
962 xvgr_subtitle(fp_tpi
, str
, oenv
);
963 xvgr_legend(fp_tpi
, 2, tpid_leg
, oenv
);
964 for (i
= nbin
- 1; i
> 0; i
--)
966 bUlogV
= -i
/ invbinw
+ bU_logV_bin_limit
- refvolshift
+ log(V_all
/ frame
);
967 fprintf(fp_tpi
, "%6.2f %10d %12.5e\n", bUlogV
, roundToInt(bin
[i
]),
968 bin
[i
] * exp(-bUlogV
) * V_all
/ VembU_all
);
976 walltime_accounting_set_nsteps_done(walltime_accounting
, frame
* inputrec
->nsteps
);