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39 * \brief This file defines the integrator for test particle insertion
41 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_mdrun
55 #include "gromacs/commandline/filenm.h"
56 #include "gromacs/domdec/dlbtiming.h"
57 #include "gromacs/domdec/domdec.h"
58 #include "gromacs/ewald/pme.h"
59 #include "gromacs/fileio/confio.h"
60 #include "gromacs/fileio/trxio.h"
61 #include "gromacs/fileio/xvgr.h"
62 #include "gromacs/gmxlib/chargegroup.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/mdatoms.h"
74 #include "gromacs/mdlib/tgroup.h"
75 #include "gromacs/mdlib/update.h"
76 #include "gromacs/mdlib/vsite.h"
77 #include "gromacs/mdrunutility/printtime.h"
78 #include "gromacs/mdtypes/commrec.h"
79 #include "gromacs/mdtypes/forcerec.h"
80 #include "gromacs/mdtypes/group.h"
81 #include "gromacs/mdtypes/inputrec.h"
82 #include "gromacs/mdtypes/md_enums.h"
83 #include "gromacs/mdtypes/mdrunoptions.h"
84 #include "gromacs/mdtypes/state.h"
85 #include "gromacs/pbcutil/pbc.h"
86 #include "gromacs/random/threefry.h"
87 #include "gromacs/random/uniformrealdistribution.h"
88 #include "gromacs/timing/wallcycle.h"
89 #include "gromacs/timing/walltime_accounting.h"
90 #include "gromacs/topology/mtop_util.h"
91 #include "gromacs/trajectory/trajectoryframe.h"
92 #include "gromacs/utility/cstringutil.h"
93 #include "gromacs/utility/fatalerror.h"
94 #include "gromacs/utility/gmxassert.h"
95 #include "gromacs/utility/logger.h"
96 #include "gromacs/utility/smalloc.h"
98 #include "legacysimulator.h"
100 //! Global max algorithm
101 static void global_max(t_commrec
*cr
, int *n
)
105 snew(sum
, cr
->nnodes
);
106 sum
[cr
->nodeid
] = *n
;
107 gmx_sumi(cr
->nnodes
, sum
, cr
);
108 for (i
= 0; i
< cr
->nnodes
; i
++)
110 *n
= std::max(*n
, sum
[i
]);
116 //! Reallocate arrays.
117 static void realloc_bins(double **bin
, int *nbin
, int nbin_new
)
121 if (nbin_new
!= *nbin
)
123 srenew(*bin
, nbin_new
);
124 for (i
= *nbin
; i
< nbin_new
; i
++)
135 // TODO: Convert to use the nbnxm kernels by putting the system and the teset molecule on two separate search grids
137 LegacySimulator::do_tpi()
140 PaddedVector
<gmx::RVec
> f
{};
141 real lambda
, t
, temp
, beta
, drmax
, epot
;
142 double embU
, sum_embU
, *sum_UgembU
, V
, V_all
, VembU_all
;
145 gmx_bool bDispCorr
, bCharge
, bRFExcl
, bNotLastFrame
, bStateChanged
, bNS
;
146 tensor force_vir
, shake_vir
, vir
, pres
;
147 int a_tp0
, a_tp1
, ngid
, gid_tp
, nener
, e
;
149 rvec mu_tot
, x_init
, dx
, x_tp
;
151 int64_t frame_step_prev
, frame_step
;
152 int64_t nsteps
, stepblocksize
= 0, step
;
155 FILE *fp_tpi
= nullptr;
156 char *ptr
, *dump_pdb
, **leg
, str
[STRLEN
], str2
[STRLEN
];
157 double dbl
, dump_ener
;
159 int nat_cavity
= 0, d
;
160 real
*mass_cavity
= nullptr, mass_tot
;
162 double invbinw
, *bin
, refvolshift
, logV
, bUlogV
;
163 gmx_bool bEnergyOutOfBounds
;
164 const char *tpid_leg
[2] = {"direct", "reweighted"};
165 auto mdatoms
= mdAtoms
->mdatoms();
167 GMX_UNUSED_VALUE(outputProvider
);
169 GMX_LOG(mdlog
.info
).asParagraph().
170 appendText("Note that it is planned to change the command gmx mdrun -tpi "
171 "(and -tpic) to make the functionality available in a different "
172 "form in a future version of GROMACS, e.g. gmx test-particle-insertion.");
174 /* Since there is no upper limit to the insertion energies,
175 * we need to set an upper limit for the distribution output.
177 real bU_bin_limit
= 50;
178 real bU_logV_bin_limit
= bU_bin_limit
+ 10;
180 if (inputrec
->cutoff_scheme
== ecutsVERLET
)
182 gmx_fatal(FARGS
, "TPI does not work (yet) with the Verlet cut-off scheme");
187 gmx_mtop_generate_local_top(*top_global
, &top
, inputrec
->efep
!= efepNO
);
189 SimulationGroups
*groups
= &top_global
->groups
;
191 bCavity
= (inputrec
->eI
== eiTPIC
);
194 ptr
= getenv("GMX_TPIC_MASSES");
201 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
202 * The center of mass of the last atoms is then used for TPIC.
205 while (sscanf(ptr
, "%20lf%n", &dbl
, &i
) > 0)
207 srenew(mass_cavity
, nat_cavity
+1);
208 mass_cavity
[nat_cavity
] = dbl
;
209 fprintf(fplog
, "mass[%d] = %f\n",
210 nat_cavity
+1, mass_cavity
[nat_cavity
]);
216 gmx_fatal(FARGS
, "Found %d masses in GMX_TPIC_MASSES", nat_cavity
);
222 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
223 state_global->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
224 /* We never need full pbc for TPI */
226 /* Determine the temperature for the Boltzmann weighting */
227 temp
= inputrec
->opts
.ref_t
[0];
230 for (i
= 1; (i
< inputrec
->opts
.ngtc
); i
++)
232 if (inputrec
->opts
.ref_t
[i
] != temp
)
234 fprintf(fplog
, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
235 fprintf(stderr
, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
239 "\n The temperature for test particle insertion is %.3f K\n\n",
242 beta
= 1.0/(BOLTZ
*temp
);
244 /* Number of insertions per frame */
245 nsteps
= inputrec
->nsteps
;
247 /* Use the same neighborlist with more insertions points
248 * in a sphere of radius drmax around the initial point
250 /* This should be a proper mdp parameter */
251 drmax
= inputrec
->rtpi
;
253 /* An environment variable can be set to dump all configurations
254 * to pdb with an insertion energy <= this value.
256 dump_pdb
= getenv("GMX_TPI_DUMP");
260 sscanf(dump_pdb
, "%20lf", &dump_ener
);
263 atoms2md(top_global
, inputrec
, -1, nullptr, top_global
->natoms
, mdAtoms
);
264 update_mdatoms(mdatoms
, inputrec
->fepvals
->init_lambda
);
266 f
.resizeWithPadding(top_global
->natoms
);
268 /* Print to log file */
269 walltime_accounting_start_time(walltime_accounting
);
270 wallcycle_start(wcycle
, ewcRUN
);
271 print_start(fplog
, cr
, walltime_accounting
, "Test Particle Insertion");
273 /* The last charge group is the group to be inserted */
274 const t_atoms
&atomsToInsert
= top_global
->moltype
[top_global
->molblock
.back().type
].atoms
;
275 a_tp0
= top_global
->natoms
- atomsToInsert
.nr
;
276 a_tp1
= top_global
->natoms
;
279 fprintf(debug
, "TPI atoms %d-%d\n", a_tp0
, a_tp1
);
282 GMX_RELEASE_ASSERT(inputrec
->rcoulomb
<= inputrec
->rlist
&& inputrec
->rvdw
<= inputrec
->rlist
, "Twin-range interactions are not supported with TPI");
284 snew(x_mol
, a_tp1
-a_tp0
);
286 bDispCorr
= (inputrec
->eDispCorr
!= edispcNO
);
288 auto x
= makeArrayRef(state_global
->x
);
289 for (i
= a_tp0
; i
< a_tp1
; i
++)
291 /* Copy the coordinates of the molecule to be insterted */
292 copy_rvec(x
[i
], x_mol
[i
-a_tp0
]);
293 /* Check if we need to print electrostatic energies */
294 bCharge
|= (mdatoms
->chargeA
[i
] != 0 ||
295 ((mdatoms
->chargeB
!= nullptr) && mdatoms
->chargeB
[i
] != 0));
297 bRFExcl
= (bCharge
&& EEL_RF(fr
->ic
->eeltype
));
299 // TODO: Calculate the center of geometry of the molecule to insert
301 calc_cgcm(fplog
, cg_tp
, cg_tp
+1, &(top
.cgs
), state_global
->x
.rvec_array(), fr
->cg_cm
);
304 if (norm(fr
->cg_cm
[cg_tp
]) > 0.5*inputrec
->rlist
&& fplog
)
306 fprintf(fplog
, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
307 fprintf(stderr
, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
312 /* Center the molecule to be inserted at zero */
313 for (i
= 0; i
< a_tp1
-a_tp0
; i
++)
315 rvec_dec(x_mol
[i
], fr
->cg_cm
[cg_tp
]);
322 fprintf(fplog
, "\nWill insert %d atoms %s partial charges\n",
323 a_tp1
-a_tp0
, bCharge
? "with" : "without");
325 fprintf(fplog
, "\nWill insert %" PRId64
" times in each frame of %s\n",
326 nsteps
, opt2fn("-rerun", nfile
, fnm
));
331 if (inputrec
->nstlist
> 1)
333 if (drmax
== 0 && a_tp1
-a_tp0
== 1)
335 gmx_fatal(FARGS
, "Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense", inputrec
->nstlist
, drmax
);
339 fprintf(fplog
, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec
->nstlist
, drmax
);
347 fprintf(fplog
, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax
);
351 ngid
= groups
->groups
[SimulationAtomGroupType::EnergyOutput
].size();
352 // TODO: Figure out which energy group to use
354 gid_tp
= GET_CGINFO_GID(fr
->cginfo
[cg_tp
]);
369 if (EEL_FULL(fr
->ic
->eeltype
))
374 snew(sum_UgembU
, nener
);
376 /* Copy the random seed set by the user */
377 seed
= inputrec
->ld_seed
;
379 gmx::ThreeFry2x64
<16> rng(seed
, gmx::RandomDomain::TestParticleInsertion
); // 16 bits internal counter => 2^16 * 2 = 131072 values per stream
380 gmx::UniformRealDistribution
<real
> dist
;
384 fp_tpi
= xvgropen(opt2fn("-tpi", nfile
, fnm
),
385 "TPI energies", "Time (ps)",
386 "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv
);
387 xvgr_subtitle(fp_tpi
, "f. are averages over one frame", oenv
);
390 sprintf(str
, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
391 leg
[e
++] = gmx_strdup(str
);
392 sprintf(str
, "f. -kT log<e\\S-\\betaU\\N>");
393 leg
[e
++] = gmx_strdup(str
);
394 sprintf(str
, "f. <e\\S-\\betaU\\N>");
395 leg
[e
++] = gmx_strdup(str
);
396 sprintf(str
, "f. V");
397 leg
[e
++] = gmx_strdup(str
);
398 sprintf(str
, "f. <Ue\\S-\\betaU\\N>");
399 leg
[e
++] = gmx_strdup(str
);
400 for (i
= 0; i
< ngid
; i
++)
402 sprintf(str
, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
403 *(groups
->groupNames
[groups
->groups
[SimulationAtomGroupType::EnergyOutput
][i
]]));
404 leg
[e
++] = gmx_strdup(str
);
408 sprintf(str
, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
409 leg
[e
++] = gmx_strdup(str
);
413 for (i
= 0; i
< ngid
; i
++)
415 sprintf(str
, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
416 *(groups
->groupNames
[groups
->groups
[SimulationAtomGroupType::EnergyOutput
][i
]]));
417 leg
[e
++] = gmx_strdup(str
);
421 sprintf(str
, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
422 leg
[e
++] = gmx_strdup(str
);
424 if (EEL_FULL(fr
->ic
->eeltype
))
426 sprintf(str
, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
427 leg
[e
++] = gmx_strdup(str
);
430 xvgr_legend(fp_tpi
, 4+nener
, leg
, oenv
);
431 for (i
= 0; i
< 4+nener
; i
++)
445 /* Avoid frame step numbers <= -1 */
446 frame_step_prev
= -1;
448 bNotLastFrame
= read_first_frame(oenv
, &status
, opt2fn("-rerun", nfile
, fnm
),
449 &rerun_fr
, TRX_NEED_X
);
452 if (rerun_fr
.natoms
- (bCavity
? nat_cavity
: 0) !=
453 mdatoms
->nr
- (a_tp1
- a_tp0
))
455 gmx_fatal(FARGS
, "Number of atoms in trajectory (%d)%s "
456 "is not equal the number in the run input file (%d) "
457 "minus the number of atoms to insert (%d)\n",
458 rerun_fr
.natoms
, bCavity
? " minus one" : "",
459 mdatoms
->nr
, a_tp1
-a_tp0
);
462 refvolshift
= log(det(rerun_fr
.box
));
464 switch (inputrec
->eI
)
467 stepblocksize
= inputrec
->nstlist
;
473 gmx_fatal(FARGS
, "Unknown integrator %s", ei_names
[inputrec
->eI
]);
476 while (bNotLastFrame
)
478 frame_step
= rerun_fr
.step
;
479 if (frame_step
<= frame_step_prev
)
481 /* We don't have step number in the trajectory file,
482 * or we have constant or decreasing step numbers.
483 * Ensure we have increasing step numbers, since we use
484 * the step numbers as a counter for random numbers.
486 frame_step
= frame_step_prev
+ 1;
488 frame_step_prev
= frame_step
;
490 lambda
= rerun_fr
.lambda
;
494 for (e
= 0; e
< nener
; e
++)
499 /* Copy the coordinates from the input trajectory */
500 auto x
= makeArrayRef(state_global
->x
);
501 for (i
= 0; i
< rerun_fr
.natoms
; i
++)
503 copy_rvec(rerun_fr
.x
[i
], x
[i
]);
505 copy_mat(rerun_fr
.box
, state_global
->box
);
507 V
= det(state_global
->box
);
510 bStateChanged
= TRUE
;
513 step
= cr
->nodeid
*stepblocksize
;
514 while (step
< nsteps
)
516 /* Restart random engine using the frame and insertion step
518 * Note that we need to draw several random values per iteration,
519 * but by using the internal subcounter functionality of ThreeFry2x64
520 * we can draw 131072 unique 64-bit values before exhausting
521 * the stream. This is a huge margin, and if something still goes
522 * wrong you will get an exception when the stream is exhausted.
524 rng
.restart(frame_step
, step
);
525 dist
.reset(); // erase any memory in the distribution
529 /* Random insertion in the whole volume */
530 bNS
= (step
% inputrec
->nstlist
== 0);
533 /* Generate a random position in the box */
534 for (d
= 0; d
< DIM
; d
++)
536 x_init
[d
] = dist(rng
)*state_global
->box
[d
][d
];
540 if (inputrec
->nstlist
== 1)
542 copy_rvec(x_init
, x_tp
);
546 /* Generate coordinates within |dx|=drmax of x_init */
549 for (d
= 0; d
< DIM
; d
++)
551 dx
[d
] = (2*dist(rng
) - 1)*drmax
;
554 while (norm2(dx
) > drmax
*drmax
);
555 rvec_add(x_init
, dx
, x_tp
);
560 /* Random insertion around a cavity location
561 * given by the last coordinate of the trajectory.
567 /* Copy the location of the cavity */
568 copy_rvec(rerun_fr
.x
[rerun_fr
.natoms
-1], x_init
);
572 /* Determine the center of mass of the last molecule */
575 for (i
= 0; i
< nat_cavity
; i
++)
577 for (d
= 0; d
< DIM
; d
++)
580 mass_cavity
[i
]*rerun_fr
.x
[rerun_fr
.natoms
-nat_cavity
+i
][d
];
582 mass_tot
+= mass_cavity
[i
];
584 for (d
= 0; d
< DIM
; d
++)
586 x_init
[d
] /= mass_tot
;
590 /* Generate coordinates within |dx|=drmax of x_init */
593 for (d
= 0; d
< DIM
; d
++)
595 dx
[d
] = (2*dist(rng
) - 1)*drmax
;
598 while (norm2(dx
) > drmax
*drmax
);
599 rvec_add(x_init
, dx
, x_tp
);
602 if (a_tp1
- a_tp0
== 1)
604 /* Insert a single atom, just copy the insertion location */
605 copy_rvec(x_tp
, x
[a_tp0
]);
609 /* Copy the coordinates from the top file */
610 for (i
= a_tp0
; i
< a_tp1
; i
++)
612 copy_rvec(x_mol
[i
-a_tp0
], x
[i
]);
614 /* Rotate the molecule randomly */
615 real angleX
= 2*M_PI
*dist(rng
);
616 real angleY
= 2*M_PI
*dist(rng
);
617 real angleZ
= 2*M_PI
*dist(rng
);
618 rotate_conf(a_tp1
-a_tp0
, state_global
->x
.rvec_array()+a_tp0
, nullptr,
619 angleX
, angleY
, angleZ
);
620 /* Shift to the insertion location */
621 for (i
= a_tp0
; i
< a_tp1
; i
++)
623 rvec_inc(x
[i
], x_tp
);
627 /* Clear some matrix variables */
628 clear_mat(force_vir
);
629 clear_mat(shake_vir
);
633 /* Set the center of geometry mass of the test molecule */
634 // TODO: Compute and set the COG
636 copy_rvec(x_init
, fr
->cg_cm
[top
.cgs
.nr
-1]);
639 /* Calc energy (no forces) on new positions.
640 * Since we only need the intermolecular energy
641 * and the RF exclusion terms of the inserted molecule occur
642 * within a single charge group we can pass NULL for the graph.
643 * This also avoids shifts that would move charge groups
645 /* Make do_force do a single node force calculation */
648 // TPI might place a particle so close that the potential
649 // is infinite. Since this is intended to happen, we
650 // temporarily suppress any exceptions that the processor
651 // might raise, then restore the old behaviour.
652 std::fenv_t floatingPointEnvironment
;
653 std::feholdexcept(&floatingPointEnvironment
);
654 do_force(fplog
, cr
, ms
, inputrec
, nullptr, nullptr, imdSession
,
656 step
, nrnb
, wcycle
, &top
,
657 state_global
->box
, state_global
->x
.arrayRefWithPadding(), &state_global
->hist
,
658 f
.arrayRefWithPadding(), force_vir
, mdatoms
, enerd
, fcd
,
659 state_global
->lambda
,
660 nullptr, fr
, ppForceWorkload
, nullptr, mu_tot
, t
, nullptr,
661 GMX_FORCE_NONBONDED
| GMX_FORCE_ENERGY
|
662 (bNS
? GMX_FORCE_DYNAMICBOX
| GMX_FORCE_NS
: 0) |
663 (bStateChanged
? GMX_FORCE_STATECHANGED
: 0),
664 DDBalanceRegionHandler(nullptr));
665 std::feclearexcept(FE_DIVBYZERO
| FE_INVALID
| FE_OVERFLOW
);
666 std::feupdateenv(&floatingPointEnvironment
);
669 bStateChanged
= FALSE
;
672 if (fr
->dispersionCorrection
)
674 /* Calculate long range corrections to pressure and energy */
675 const DispersionCorrection::Correction correction
=
676 fr
->dispersionCorrection
->calculate(state_global
->box
, lambda
);
677 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
678 enerd
->term
[F_DISPCORR
] = correction
.energy
;
679 enerd
->term
[F_EPOT
] += correction
.energy
;
680 enerd
->term
[F_PRES
] += correction
.pressure
;
681 enerd
->term
[F_DVDL
] += correction
.dvdl
;
685 enerd
->term
[F_DISPCORR
] = 0;
688 epot
= enerd
->term
[F_EPOT
];
689 bEnergyOutOfBounds
= FALSE
;
691 /* If the compiler doesn't optimize this check away
692 * we catch the NAN energies.
693 * The epot>GMX_REAL_MAX check catches inf values,
694 * which should nicely result in embU=0 through the exp below,
695 * but it does not hurt to check anyhow.
697 /* Non-bonded Interaction usually diverge at r=0.
698 * With tabulated interaction functions the first few entries
699 * should be capped in a consistent fashion between
700 * repulsion, dispersion and Coulomb to avoid accidental
701 * negative values in the total energy.
702 * The table generation code in tables.c does this.
703 * With user tbales the user should take care of this.
705 if (epot
!= epot
|| epot
> GMX_REAL_MAX
)
707 bEnergyOutOfBounds
= TRUE
;
709 if (bEnergyOutOfBounds
)
713 fprintf(debug
, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t
, static_cast<int>(step
), epot
);
719 // Exponent argument is fine in SP range, but output can be in DP range
720 embU
= exp(static_cast<double>(-beta
*epot
));
722 /* Determine the weighted energy contributions of each energy group */
724 sum_UgembU
[e
++] += epot
*embU
;
727 for (i
= 0; i
< ngid
; i
++)
730 enerd
->grpp
.ener
[egBHAMSR
][GID(i
, gid_tp
, ngid
)]*embU
;
735 for (i
= 0; i
< ngid
; i
++)
738 enerd
->grpp
.ener
[egLJSR
][GID(i
, gid_tp
, ngid
)]*embU
;
743 sum_UgembU
[e
++] += enerd
->term
[F_DISPCORR
]*embU
;
747 for (i
= 0; i
< ngid
; i
++)
749 sum_UgembU
[e
++] += enerd
->grpp
.ener
[egCOULSR
][GID(i
, gid_tp
, ngid
)] * embU
;
753 sum_UgembU
[e
++] += enerd
->term
[F_RF_EXCL
]*embU
;
755 if (EEL_FULL(fr
->ic
->eeltype
))
757 sum_UgembU
[e
++] += enerd
->term
[F_COUL_RECIP
]*embU
;
762 if (embU
== 0 || beta
*epot
> bU_bin_limit
)
768 i
= gmx::roundToInt((bU_logV_bin_limit
769 - (beta
*epot
- logV
+ refvolshift
))*invbinw
);
776 realloc_bins(&bin
, &nbin
, i
+10);
783 fprintf(debug
, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
784 static_cast<int>(step
), epot
, x_tp
[XX
], x_tp
[YY
], x_tp
[ZZ
]);
787 if (dump_pdb
&& epot
<= dump_ener
)
789 sprintf(str
, "t%g_step%d.pdb", t
, static_cast<int>(step
));
790 sprintf(str2
, "t: %f step %d ener: %f", t
, static_cast<int>(step
), epot
);
791 write_sto_conf_mtop(str
, str2
, top_global
, state_global
->x
.rvec_array(), state_global
->v
.rvec_array(),
792 inputrec
->ePBC
, state_global
->box
);
796 if ((step
/stepblocksize
) % cr
->nnodes
!= cr
->nodeid
)
798 /* Skip all steps assigned to the other MPI ranks */
799 step
+= (cr
->nnodes
- 1)*stepblocksize
;
805 /* When running in parallel sum the energies over the processes */
806 gmx_sumd(1, &sum_embU
, cr
);
807 gmx_sumd(nener
, sum_UgembU
, cr
);
812 VembU_all
+= V
*sum_embU
/nsteps
;
816 if (mdrunOptions
.verbose
|| frame
%10 == 0 || frame
< 10)
818 fprintf(stderr
, "mu %10.3e <mu> %10.3e\n",
819 -log(sum_embU
/nsteps
)/beta
, -log(VembU_all
/V_all
)/beta
);
822 fprintf(fp_tpi
, "%10.3f %12.5e %12.5e %12.5e %12.5e",
824 VembU_all
== 0 ? 20/beta
: -log(VembU_all
/V_all
)/beta
,
825 sum_embU
== 0 ? 20/beta
: -log(sum_embU
/nsteps
)/beta
,
827 for (e
= 0; e
< nener
; e
++)
829 fprintf(fp_tpi
, " %12.5e", sum_UgembU
[e
]/nsteps
);
831 fprintf(fp_tpi
, "\n");
835 bNotLastFrame
= read_next_frame(oenv
, status
, &rerun_fr
);
836 } /* End of the loop */
837 walltime_accounting_end_time(walltime_accounting
);
841 if (fp_tpi
!= nullptr)
846 if (fplog
!= nullptr)
848 fprintf(fplog
, "\n");
849 fprintf(fplog
, " <V> = %12.5e nm^3\n", V_all
/frame
);
850 const double mu
= -log(VembU_all
/V_all
)/beta
;
851 fprintf(fplog
, " <mu> = %12.5e kJ/mol\n", mu
);
853 if (!std::isfinite(mu
))
855 fprintf(fplog
, "\nThe computed chemical potential is not finite - consider increasing the number of steps and/or the number of frames to insert into.\n");
859 /* Write the Boltzmann factor histogram */
862 /* When running in parallel sum the bins over the processes */
865 realloc_bins(&bin
, &nbin
, i
);
866 gmx_sumd(nbin
, bin
, cr
);
870 fp_tpi
= xvgropen(opt2fn("-tpid", nfile
, fnm
),
871 "TPI energy distribution",
872 "\\betaU - log(V/<V>)", "count", oenv
);
873 sprintf(str
, "number \\betaU > %g: %9.3e", bU_bin_limit
, bin
[0]);
874 xvgr_subtitle(fp_tpi
, str
, oenv
);
875 xvgr_legend(fp_tpi
, 2, tpid_leg
, oenv
);
876 for (i
= nbin
-1; i
> 0; i
--)
878 bUlogV
= -i
/invbinw
+ bU_logV_bin_limit
- refvolshift
+ log(V_all
/frame
);
879 fprintf(fp_tpi
, "%6.2f %10d %12.5e\n",
882 bin
[i
]*exp(-bUlogV
)*V_all
/VembU_all
);
890 walltime_accounting_set_nsteps_done(walltime_accounting
, frame
*inputrec
->nsteps
);