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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
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/conformation_utilities.h"
63 #include "gromacs/gmxlib/network.h"
64 #include "gromacs/gmxlib/nrnb.h"
65 #include "gromacs/math/units.h"
66 #include "gromacs/math/vec.h"
67 #include "gromacs/mdlib/constr.h"
68 #include "gromacs/mdlib/dispersioncorrection.h"
69 #include "gromacs/mdlib/energyoutput.h"
70 #include "gromacs/mdlib/force.h"
71 #include "gromacs/mdlib/force_flags.h"
72 #include "gromacs/mdlib/gmx_omp_nthreads.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/forcebuffers.h"
80 #include "gromacs/mdtypes/forcerec.h"
81 #include "gromacs/mdtypes/group.h"
82 #include "gromacs/mdtypes/inputrec.h"
83 #include "gromacs/mdtypes/interaction_const.h"
84 #include "gromacs/mdtypes/md_enums.h"
85 #include "gromacs/mdtypes/mdatom.h"
86 #include "gromacs/mdtypes/mdrunoptions.h"
87 #include "gromacs/mdtypes/state.h"
88 #include "gromacs/nbnxm/nbnxm.h"
89 #include "gromacs/pbcutil/pbc.h"
90 #include "gromacs/random/threefry.h"
91 #include "gromacs/random/uniformrealdistribution.h"
92 #include "gromacs/timing/wallcycle.h"
93 #include "gromacs/timing/walltime_accounting.h"
94 #include "gromacs/topology/mtop_util.h"
95 #include "gromacs/trajectory/trajectoryframe.h"
96 #include "gromacs/utility/cstringutil.h"
97 #include "gromacs/utility/fatalerror.h"
98 #include "gromacs/utility/gmxassert.h"
99 #include "gromacs/utility/logger.h"
100 #include "gromacs/utility/smalloc.h"
102 #include "legacysimulator.h"
104 //! Global max algorithm
105 static void global_max(t_commrec* cr, int* n)
109 snew(sum, cr->nnodes);
110 sum[cr->nodeid] = *n;
111 gmx_sumi(cr->nnodes, sum, cr);
112 for (i = 0; i < cr->nnodes; i++)
114 *n = std::max(*n, sum[i]);
120 //! Reallocate arrays.
121 static void realloc_bins(double** bin, int* nbin, int nbin_new)
125 if (nbin_new != *nbin)
127 srenew(*bin, nbin_new);
128 for (i = *nbin; i < nbin_new; i++)
136 //! Computes and returns the RF exclusion energy for the last molecule starting at \p beginAtom
137 static real reactionFieldExclusionCorrection(gmx::ArrayRef<const gmx::RVec> x,
138 const t_mdatoms& mdatoms,
139 const interaction_const_t& ic,
144 for (int i = beginAtom; i < mdatoms.homenr; i++)
146 const real qi = mdatoms.chargeA[i];
147 energy -= 0.5 * qi * qi * ic.reactionFieldShift;
149 for (int j = i + 1; j < mdatoms.homenr; j++)
151 const real qj = mdatoms.chargeA[j];
152 const real rsq = distance2(x[i], x[j]);
153 energy += qi * qj * (ic.reactionFieldCoefficient * rsq - ic.reactionFieldShift);
157 return ic.epsfac * energy;
163 // TODO: Convert to use the nbnxm kernels by putting the system and the teset molecule on two separate search grids
164 void LegacySimulator::do_tpi()
166 GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault) == 1, "TPI does not support OpenMP");
168 gmx_localtop_t top(top_global->ffparams);
170 real lambda, t, temp, beta, drmax, epot;
171 double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
174 gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
175 tensor force_vir, shake_vir, vir, pres;
176 int a_tp0, a_tp1, ngid, gid_tp, nener, e;
178 rvec mu_tot, x_init, dx;
180 int64_t frame_step_prev, frame_step;
181 int64_t nsteps, stepblocksize = 0, step;
184 FILE* fp_tpi = nullptr;
185 char * ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
186 double dbl, dump_ener;
188 int nat_cavity = 0, d;
189 real * mass_cavity = nullptr, mass_tot;
191 double invbinw, *bin, refvolshift, logV, bUlogV;
192 gmx_bool bEnergyOutOfBounds;
193 const char* tpid_leg[2] = { "direct", "reweighted" };
194 auto mdatoms = mdAtoms->mdatoms();
196 GMX_UNUSED_VALUE(outputProvider);
198 if (EVDW_PME(inputrec->vdwtype))
200 gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
202 if (haveEwaldSurfaceContribution(*inputrec))
205 "TPI with PME currently only works in a 3D geometry with tin-foil "
206 "boundary conditions");
212 "Note that it is planned to change the command gmx mdrun -tpi "
213 "(and -tpic) to make the functionality available in a different "
214 "form in a future version of GROMACS, e.g. gmx test-particle-insertion.");
216 /* Since there is no upper limit to the insertion energies,
217 * we need to set an upper limit for the distribution output.
219 real bU_bin_limit = 50;
220 real bU_logV_bin_limit = bU_bin_limit + 10;
224 gmx_mtop_generate_local_top(*top_global, &top, inputrec->efep != FreeEnergyPerturbationType::No);
226 const SimulationGroups* groups = &top_global->groups;
228 bCavity = (inputrec->eI == IntegrationAlgorithm::TPIC);
231 ptr = getenv("GMX_TPIC_MASSES");
238 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
239 * The center of mass of the last atoms is then used for TPIC.
242 while (sscanf(ptr, "%20lf%n", &dbl, &i) > 0)
244 srenew(mass_cavity, nat_cavity + 1);
245 mass_cavity[nat_cavity] = dbl;
246 fprintf(fplog, "mass[%d] = %f\n", nat_cavity + 1, mass_cavity[nat_cavity]);
252 gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity);
258 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
259 state_global->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
260 /* We never need full pbc for TPI */
261 fr->pbcType = PbcType::Xyz;
262 /* Determine the temperature for the Boltzmann weighting */
263 temp = inputrec->opts.ref_t[0];
266 for (i = 1; (i < inputrec->opts.ngtc); i++)
268 if (inputrec->opts.ref_t[i] != temp)
271 "\nWARNING: The temperatures of the different temperature coupling groups "
272 "are not identical\n\n");
274 "\nWARNING: The temperatures of the different temperature coupling groups "
275 "are not identical\n\n");
278 fprintf(fplog, "\n The temperature for test particle insertion is %.3f K\n\n", temp);
280 beta = 1.0 / (gmx::c_boltz * temp);
282 /* Number of insertions per frame */
283 nsteps = inputrec->nsteps;
285 /* Use the same neighborlist with more insertions points
286 * in a sphere of radius drmax around the initial point
288 /* This should be a proper mdp parameter */
289 drmax = inputrec->rtpi;
291 /* An environment variable can be set to dump all configurations
292 * to pdb with an insertion energy <= this value.
294 dump_pdb = getenv("GMX_TPI_DUMP");
298 sscanf(dump_pdb, "%20lf", &dump_ener);
301 atoms2md(top_global, inputrec, -1, {}, top_global->natoms, mdAtoms);
302 update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
304 f.resize(top_global->natoms);
306 /* Print to log file */
307 walltime_accounting_start_time(walltime_accounting);
308 wallcycle_start(wcycle, ewcRUN);
309 print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
311 /* The last charge group is the group to be inserted */
312 const t_atoms& atomsToInsert = top_global->moltype[top_global->molblock.back().type].atoms;
313 a_tp0 = top_global->natoms - atomsToInsert.nr;
314 a_tp1 = top_global->natoms;
317 fprintf(debug, "TPI atoms %d-%d\n", a_tp0, a_tp1);
320 auto x = makeArrayRef(state_global->x);
322 if (EEL_PME(fr->ic->eeltype))
324 gmx_pme_reinit_atoms(fr->pmedata, a_tp0, nullptr, nullptr);
327 /* With reacion-field we have distance dependent potentials
328 * between excluded atoms, we need to add these separately
329 * for the inserted molecule.
331 real rfExclusionEnergy = 0;
332 if (EEL_RF(fr->ic->eeltype))
334 rfExclusionEnergy = reactionFieldExclusionCorrection(x, *mdatoms, *fr->ic, a_tp0);
337 fprintf(debug, "RF exclusion correction for inserted molecule: %f kJ/mol\n", rfExclusionEnergy);
341 snew(x_mol, a_tp1 - a_tp0);
343 bDispCorr = (inputrec->eDispCorr != DispersionCorrectionType::No);
345 for (i = a_tp0; i < a_tp1; i++)
347 /* Copy the coordinates of the molecule to be insterted */
348 copy_rvec(x[i], x_mol[i - a_tp0]);
349 /* Check if we need to print electrostatic energies */
350 bCharge |= (mdatoms->chargeA[i] != 0
351 || ((mdatoms->chargeB != nullptr) && mdatoms->chargeB[i] != 0));
353 bRFExcl = (bCharge && EEL_RF(fr->ic->eeltype));
355 // Calculate the center of geometry of the molecule to insert
356 rvec cog = { 0, 0, 0 };
357 for (int a = a_tp0; a < a_tp1; a++)
361 svmul(1.0_real / (a_tp1 - a_tp0), cog, cog);
363 for (int a = a_tp0; a < a_tp1; a++)
365 molRadius = std::max(molRadius, distance2(x[a], cog));
367 molRadius = std::sqrt(molRadius);
369 const real maxCutoff = std::max(inputrec->rvdw, inputrec->rcoulomb);
372 if (norm(cog) > 0.5 * maxCutoff && fplog)
374 fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
375 fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
380 /* Center the molecule to be inserted at zero */
381 for (i = 0; i < a_tp1 - a_tp0; i++)
383 rvec_dec(x_mol[i], cog);
389 fprintf(fplog, "\nWill insert %d atoms %s partial charges\n", a_tp1 - a_tp0, bCharge ? "with" : "without");
392 "\nWill insert %" PRId64 " times in each frame of %s\n",
394 opt2fn("-rerun", nfile, fnm));
399 if (inputrec->nstlist > 1)
402 /* With the same pair list we insert in a sphere of radius rtpi in different orientations */
403 if (drmax == 0 && a_tp1 - a_tp0 == 1)
406 "Re-using the neighborlist %d times for insertions of a single atom in a "
407 "sphere of radius %f does not make sense",
414 "Will use the same neighborlist for %d insertions in a sphere of radius "
426 "Will insert randomly in a sphere of radius %f around the center of the "
432 /* With the same pair list we insert in a sphere of radius rtpi
433 * in different orientations. We generate the pairlist with all
434 * inserted atoms located in the center of the sphere, so we need
435 * a buffer of size of the sphere and molecule radius.
438 // TODO: Avoid changing inputrec (#3854)
439 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
440 nonConstInputrec->rlist = maxCutoff + 2 * inputrec->rtpi + 2 * molRadius;
442 fr->rlist = inputrec->rlist;
443 fr->nbv->changePairlistRadii(inputrec->rlist, inputrec->rlist);
445 ngid = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
446 gid_tp = GET_CGINFO_GID(fr->cginfo[a_tp0]);
447 for (int a = a_tp0 + 1; a < a_tp1; a++)
449 if (GET_CGINFO_GID(fr->cginfo[a]) != gid_tp)
452 "NOTE: Atoms in the molecule to insert belong to different energy groups.\n"
453 " Only contributions to the group of the first atom will be reported.\n");
469 if (EEL_FULL(fr->ic->eeltype))
474 snew(sum_UgembU, nener);
476 /* Copy the random seed set by the user */
477 seed = inputrec->ld_seed;
479 gmx::ThreeFry2x64<16> rng(
480 seed, gmx::RandomDomain::TestParticleInsertion); // 16 bits internal counter => 2^16 * 2 = 131072 values per stream
481 gmx::UniformRealDistribution<real> dist;
485 fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
488 "(kJ mol\\S-1\\N) / (nm\\S3\\N)",
490 xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
491 snew(leg, 4 + nener);
493 sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
494 leg[e++] = gmx_strdup(str);
495 sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
496 leg[e++] = gmx_strdup(str);
497 sprintf(str, "f. <e\\S-\\betaU\\N>");
498 leg[e++] = gmx_strdup(str);
499 sprintf(str, "f. V");
500 leg[e++] = gmx_strdup(str);
501 sprintf(str, "f. <Ue\\S-\\betaU\\N>");
502 leg[e++] = gmx_strdup(str);
503 for (i = 0; i < ngid; i++)
506 "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
507 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][i]]));
508 leg[e++] = gmx_strdup(str);
512 sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
513 leg[e++] = gmx_strdup(str);
517 for (i = 0; i < ngid; i++)
520 "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
521 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][i]]));
522 leg[e++] = gmx_strdup(str);
526 sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
527 leg[e++] = gmx_strdup(str);
529 if (EEL_FULL(fr->ic->eeltype))
531 sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
532 leg[e++] = gmx_strdup(str);
535 xvgr_legend(fp_tpi, 4 + nener, leg, oenv);
536 for (i = 0; i < 4 + nener; i++)
550 /* Avoid frame step numbers <= -1 */
551 frame_step_prev = -1;
553 bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
556 if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) != mdatoms->nr - (a_tp1 - a_tp0))
559 "Number of atoms in trajectory (%d)%s "
560 "is not equal the number in the run input file (%d) "
561 "minus the number of atoms to insert (%d)\n",
563 bCavity ? " minus one" : "",
568 refvolshift = log(det(rerun_fr.box));
570 switch (inputrec->eI)
572 case IntegrationAlgorithm::TPI: stepblocksize = inputrec->nstlist; break;
573 case IntegrationAlgorithm::TPIC: stepblocksize = 1; break;
574 default: gmx_fatal(FARGS, "Unknown integrator %s", enumValueToString(inputrec->eI));
577 while (bNotLastFrame)
579 frame_step = rerun_fr.step;
580 if (frame_step <= frame_step_prev)
582 /* We don't have step number in the trajectory file,
583 * or we have constant or decreasing step numbers.
584 * Ensure we have increasing step numbers, since we use
585 * the step numbers as a counter for random numbers.
587 frame_step = frame_step_prev + 1;
589 frame_step_prev = frame_step;
591 lambda = rerun_fr.lambda;
595 for (e = 0; e < nener; e++)
600 /* Copy the coordinates from the input trajectory */
601 auto x = makeArrayRef(state_global->x);
602 for (i = 0; i < rerun_fr.natoms; i++)
604 copy_rvec(rerun_fr.x[i], x[i]);
606 copy_mat(rerun_fr.box, state_global->box);
607 const matrix& box = state_global->box;
612 bStateChanged = TRUE;
615 put_atoms_in_box(fr->pbcType, box, x);
617 /* Put all atoms except for the inserted ones on the grid */
618 rvec vzero = { 0, 0, 0 };
619 rvec boxDiagonal = { box[XX][XX], box[YY][YY], box[ZZ][ZZ] };
621 fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1, fr->cginfo, x, 0, nullptr);
623 step = cr->nodeid * stepblocksize;
624 while (step < nsteps)
626 /* Restart random engine using the frame and insertion step
628 * Note that we need to draw several random values per iteration,
629 * but by using the internal subcounter functionality of ThreeFry2x64
630 * we can draw 131072 unique 64-bit values before exhausting
631 * the stream. This is a huge margin, and if something still goes
632 * wrong you will get an exception when the stream is exhausted.
634 rng.restart(frame_step, step);
635 dist.reset(); // erase any memory in the distribution
639 /* Random insertion in the whole volume */
640 bNS = (step % inputrec->nstlist == 0);
643 /* Generate a random position in the box */
644 for (d = 0; d < DIM; d++)
646 x_init[d] = dist(rng) * state_global->box[d][d];
652 /* Random insertion around a cavity location
653 * given by the last coordinate of the trajectory.
659 /* Copy the location of the cavity */
660 copy_rvec(rerun_fr.x[rerun_fr.natoms - 1], x_init);
664 /* Determine the center of mass of the last molecule */
667 for (i = 0; i < nat_cavity; i++)
669 for (d = 0; d < DIM; d++)
671 x_init[d] += mass_cavity[i]
672 * rerun_fr.x[rerun_fr.natoms - nat_cavity + i][d];
674 mass_tot += mass_cavity[i];
676 for (d = 0; d < DIM; d++)
678 x_init[d] /= mass_tot;
686 for (int a = a_tp0; a < a_tp1; a++)
691 /* Put the inserted molecule on it's own search grid */
693 fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 }, -1, fr->cginfo, x, 0, nullptr);
695 /* TODO: Avoid updating all atoms at every bNS step */
696 fr->nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
697 gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
700 fr->nbv->constructPairlist(InteractionLocality::Local, top.excls, step, nrnb);
705 /* Add random displacement uniformly distributed in a sphere
706 * of radius rtpi. We don't need to do this is we generate
707 * a new center location every step.
710 if (bCavity || inputrec->nstlist > 1)
712 /* Generate coordinates within |dx|=drmax of x_init */
715 for (d = 0; d < DIM; d++)
717 dx[d] = (2 * dist(rng) - 1) * drmax;
719 } while (norm2(dx) > drmax * drmax);
720 rvec_add(x_init, dx, x_tp);
724 copy_rvec(x_init, x_tp);
727 if (a_tp1 - a_tp0 == 1)
729 /* Insert a single atom, just copy the insertion location */
730 copy_rvec(x_tp, x[a_tp0]);
734 /* Copy the coordinates from the top file */
735 for (i = a_tp0; i < a_tp1; i++)
737 copy_rvec(x_mol[i - a_tp0], x[i]);
739 /* Rotate the molecule randomly */
740 real angleX = 2 * M_PI * dist(rng);
741 real angleY = 2 * M_PI * dist(rng);
742 real angleZ = 2 * M_PI * dist(rng);
743 rotate_conf(a_tp1 - a_tp0, state_global->x.rvec_array() + a_tp0, nullptr, angleX, angleY, angleZ);
744 /* Shift to the insertion location */
745 for (i = a_tp0; i < a_tp1; i++)
747 rvec_inc(x[i], x_tp);
751 /* Note: NonLocal refers to the inserted molecule */
752 fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
754 /* Clear some matrix variables */
755 clear_mat(force_vir);
756 clear_mat(shake_vir);
760 /* Calc energy (no forces) on new positions. */
761 /* Make do_force do a single node force calculation */
764 // TPI might place a particle so close that the potential
765 // is infinite. Since this is intended to happen, we
766 // temporarily suppress any exceptions that the processor
767 // might raise, then restore the old behaviour.
768 std::fenv_t floatingPointEnvironment;
769 std::feholdexcept(&floatingPointEnvironment);
783 state_global->x.arrayRefWithPadding(),
789 state_global->lambda,
796 GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
797 DDBalanceRegionHandler(nullptr));
798 std::feclearexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
799 std::feupdateenv(&floatingPointEnvironment);
802 bStateChanged = FALSE;
804 if (fr->dispersionCorrection)
806 /* Calculate long range corrections to pressure and energy */
807 const DispersionCorrection::Correction correction =
808 fr->dispersionCorrection->calculate(state_global->box, lambda);
809 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
810 enerd->term[F_DISPCORR] = correction.energy;
811 enerd->term[F_EPOT] += correction.energy;
812 enerd->term[F_PRES] += correction.pressure;
813 enerd->term[F_DVDL] += correction.dvdl;
817 enerd->term[F_DISPCORR] = 0;
819 if (EEL_RF(fr->ic->eeltype))
821 enerd->term[F_EPOT] += rfExclusionEnergy;
824 epot = enerd->term[F_EPOT];
825 bEnergyOutOfBounds = FALSE;
827 /* If the compiler doesn't optimize this check away
828 * we catch the NAN energies.
829 * The epot>GMX_REAL_MAX check catches inf values,
830 * which should nicely result in embU=0 through the exp below,
831 * but it does not hurt to check anyhow.
833 /* Non-bonded Interaction usually diverge at r=0.
834 * With tabulated interaction functions the first few entries
835 * should be capped in a consistent fashion between
836 * repulsion, dispersion and Coulomb to avoid accidental
837 * negative values in the total energy.
838 * The table generation code in tables.c does this.
839 * With user tbales the user should take care of this.
841 if (epot != epot || epot > GMX_REAL_MAX)
843 bEnergyOutOfBounds = TRUE;
845 if (bEnergyOutOfBounds)
850 "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n",
852 static_cast<int>(step),
859 // Exponent argument is fine in SP range, but output can be in DP range
860 embU = exp(static_cast<double>(-beta * epot));
862 /* Determine the weighted energy contributions of each energy group */
864 sum_UgembU[e++] += epot * embU;
867 for (i = 0; i < ngid; i++)
869 sum_UgembU[e++] += enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] * embU;
874 for (i = 0; i < ngid; i++)
876 sum_UgembU[e++] += enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] * embU;
881 sum_UgembU[e++] += enerd->term[F_DISPCORR] * embU;
885 for (i = 0; i < ngid; i++)
887 sum_UgembU[e++] += enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] * embU;
891 sum_UgembU[e++] += rfExclusionEnergy * embU;
893 if (EEL_FULL(fr->ic->eeltype))
895 sum_UgembU[e++] += enerd->term[F_COUL_RECIP] * embU;
900 if (embU == 0 || beta * epot > bU_bin_limit)
906 i = gmx::roundToInt((bU_logV_bin_limit - (beta * epot - logV + refvolshift)) * invbinw);
913 realloc_bins(&bin, &nbin, i + 10);
921 "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
922 static_cast<int>(step),
929 if (dump_pdb && epot <= dump_ener)
931 sprintf(str, "t%g_step%d.pdb", t, static_cast<int>(step));
932 sprintf(str2, "t: %f step %d ener: %f", t, static_cast<int>(step), epot);
933 write_sto_conf_mtop(str,
936 state_global->x.rvec_array(),
937 state_global->v.rvec_array(),
943 if ((step / stepblocksize) % cr->nnodes != cr->nodeid)
945 /* Skip all steps assigned to the other MPI ranks */
946 step += (cr->nnodes - 1) * stepblocksize;
952 /* When running in parallel sum the energies over the processes */
953 gmx_sumd(1, &sum_embU, cr);
954 gmx_sumd(nener, sum_UgembU, cr);
959 VembU_all += V * sum_embU / nsteps;
963 if (mdrunOptions.verbose || frame % 10 == 0 || frame < 10)
966 "mu %10.3e <mu> %10.3e\n",
967 -log(sum_embU / nsteps) / beta,
968 -log(VembU_all / V_all) / beta);
972 "%10.3f %12.5e %12.5e %12.5e %12.5e",
974 VembU_all == 0 ? 20 / beta : -log(VembU_all / V_all) / beta,
975 sum_embU == 0 ? 20 / beta : -log(sum_embU / nsteps) / beta,
978 for (e = 0; e < nener; e++)
980 fprintf(fp_tpi, " %12.5e", sum_UgembU[e] / nsteps);
982 fprintf(fp_tpi, "\n");
986 bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
987 } /* End of the loop */
988 walltime_accounting_end_time(walltime_accounting);
992 if (fp_tpi != nullptr)
997 if (fplog != nullptr)
999 fprintf(fplog, "\n");
1000 fprintf(fplog, " <V> = %12.5e nm^3\n", V_all / frame);
1001 const double mu = -log(VembU_all / V_all) / beta;
1002 fprintf(fplog, " <mu> = %12.5e kJ/mol\n", mu);
1004 if (!std::isfinite(mu))
1007 "\nThe computed chemical potential is not finite - consider increasing the "
1008 "number of steps and/or the number of frames to insert into.\n");
1012 /* Write the Boltzmann factor histogram */
1015 /* When running in parallel sum the bins over the processes */
1018 realloc_bins(&bin, &nbin, i);
1019 gmx_sumd(nbin, bin, cr);
1023 fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
1024 "TPI energy distribution",
1025 "\\betaU - log(V/<V>)",
1028 sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
1029 xvgr_subtitle(fp_tpi, str, oenv);
1030 xvgr_legend(fp_tpi, 2, tpid_leg, oenv);
1031 for (i = nbin - 1; i > 0; i--)
1033 bUlogV = -i / invbinw + bU_logV_bin_limit - refvolshift + log(V_all / frame);
1034 fprintf(fp_tpi, "%6.2f %10d %12.5e\n", bUlogV, roundToInt(bin[i]), bin[i] * exp(-bUlogV) * V_all / VembU_all);
1042 walltime_accounting_set_nsteps_done(walltime_accounting, frame * inputrec->nsteps);