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50 #include "chargegroup.h"
54 #include "gmx_fatal.h"
67 #include "gromacs/random/random.h"
72 #include "mtop_util.h"
74 #include "gromacs/gmxlib/conformation-utilities.h"
76 #include "gromacs/fileio/confio.h"
77 #include "gromacs/fileio/gmxfio.h"
78 #include "gromacs/fileio/trxio.h"
79 #include "gromacs/timing/wallcycle.h"
80 #include "gromacs/timing/walltime_accounting.h"
82 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
83 #include "gromacs/simd/general_x86_sse2.h"
87 static void global_max(t_commrec *cr, int *n)
91 snew(sum, cr->nnodes);
93 gmx_sumi(cr->nnodes, sum, cr);
94 for (i = 0; i < cr->nnodes; i++)
102 static void realloc_bins(double **bin, int *nbin, int nbin_new)
106 if (nbin_new != *nbin)
108 srenew(*bin, nbin_new);
109 for (i = *nbin; i < nbin_new; i++)
117 double do_tpi(FILE *fplog, t_commrec *cr,
118 int nfile, const t_filenm fnm[],
119 const output_env_t oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
120 int gmx_unused nstglobalcomm,
121 gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr,
122 int gmx_unused stepout,
123 t_inputrec *inputrec,
124 gmx_mtop_t *top_global, t_fcdata *fcd,
127 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
128 gmx_edsam_t gmx_unused ed,
130 int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
131 gmx_membed_t gmx_unused membed,
132 real gmx_unused cpt_period, real gmx_unused max_hours,
133 const char gmx_unused *deviceOptions,
134 unsigned long gmx_unused Flags,
135 gmx_walltime_accounting_t walltime_accounting)
137 const char *TPI = "Test Particle Insertion";
139 gmx_groups_t *groups;
140 gmx_enerdata_t *enerd;
142 real lambda, t, temp, beta, drmax, epot;
143 double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
146 gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS, bOurStep;
147 tensor force_vir, shake_vir, vir, pres;
148 int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
150 rvec mu_tot, x_init, dx, x_tp;
151 int nnodes, frame, nsteps, step;
155 char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
156 double dbl, dump_ener;
158 int nat_cavity = 0, d;
159 real *mass_cavity = NULL, mass_tot;
161 double invbinw, *bin, refvolshift, logV, bUlogV;
162 real dvdl, prescorr, enercorr, dvdlcorr;
163 gmx_bool bEnergyOutOfBounds;
164 const char *tpid_leg[2] = {"direct", "reweighted"};
166 /* Since there is no upper limit to the insertion energies,
167 * we need to set an upper limit for the distribution output.
169 real bU_bin_limit = 50;
170 real bU_logV_bin_limit = bU_bin_limit + 10;
174 top = gmx_mtop_generate_local_top(top_global, inputrec);
176 groups = &top_global->groups;
178 bCavity = (inputrec->eI == eiTPIC);
181 ptr = getenv("GMX_TPIC_MASSES");
188 /* Read (multiple) masses from env var GMX_TPIC_MASSES,
189 * The center of mass of the last atoms is then used for TPIC.
192 while (sscanf(ptr, "%lf%n", &dbl, &i) > 0)
194 srenew(mass_cavity, nat_cavity+1);
195 mass_cavity[nat_cavity] = dbl;
196 fprintf(fplog, "mass[%d] = %f\n",
197 nat_cavity+1, mass_cavity[nat_cavity]);
203 gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity);
209 init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
210 state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
211 /* We never need full pbc for TPI */
213 /* Determine the temperature for the Boltzmann weighting */
214 temp = inputrec->opts.ref_t[0];
217 for (i = 1; (i < inputrec->opts.ngtc); i++)
219 if (inputrec->opts.ref_t[i] != temp)
221 fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
222 fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
226 "\n The temperature for test particle insertion is %.3f K\n\n",
229 beta = 1.0/(BOLTZ*temp);
231 /* Number of insertions per frame */
232 nsteps = inputrec->nsteps;
234 /* Use the same neighborlist with more insertions points
235 * in a sphere of radius drmax around the initial point
237 /* This should be a proper mdp parameter */
238 drmax = inputrec->rtpi;
240 /* An environment variable can be set to dump all configurations
241 * to pdb with an insertion energy <= this value.
243 dump_pdb = getenv("GMX_TPI_DUMP");
247 sscanf(dump_pdb, "%lf", &dump_ener);
250 atoms2md(top_global, inputrec, 0, NULL, 0, top_global->natoms, mdatoms);
251 update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
254 init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
255 snew(f, top_global->natoms);
257 /* Print to log file */
258 walltime_accounting_start(walltime_accounting);
259 wallcycle_start(wcycle, ewcRUN);
260 print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
262 /* The last charge group is the group to be inserted */
263 cg_tp = top->cgs.nr - 1;
264 a_tp0 = top->cgs.index[cg_tp];
265 a_tp1 = top->cgs.index[cg_tp+1];
268 fprintf(debug, "TPI cg %d, atoms %d-%d\n", cg_tp, a_tp0, a_tp1);
270 if (a_tp1 - a_tp0 > 1 &&
271 (inputrec->rlist < inputrec->rcoulomb ||
272 inputrec->rlist < inputrec->rvdw))
274 gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off");
276 snew(x_mol, a_tp1-a_tp0);
278 bDispCorr = (inputrec->eDispCorr != edispcNO);
280 for (i = a_tp0; i < a_tp1; i++)
282 /* Copy the coordinates of the molecule to be insterted */
283 copy_rvec(state->x[i], x_mol[i-a_tp0]);
284 /* Check if we need to print electrostatic energies */
285 bCharge |= (mdatoms->chargeA[i] != 0 ||
286 (mdatoms->chargeB && mdatoms->chargeB[i] != 0));
288 bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype != eelRF_NEC);
290 calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state->x, fr->cg_cm);
293 if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog)
295 fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
296 fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
301 /* Center the molecule to be inserted at zero */
302 for (i = 0; i < a_tp1-a_tp0; i++)
304 rvec_dec(x_mol[i], fr->cg_cm[cg_tp]);
310 fprintf(fplog, "\nWill insert %d atoms %s partial charges\n",
311 a_tp1-a_tp0, bCharge ? "with" : "without");
313 fprintf(fplog, "\nWill insert %d times in each frame of %s\n",
314 nsteps, opt2fn("-rerun", nfile, fnm));
319 if (inputrec->nstlist > 1)
321 if (drmax == 0 && a_tp1-a_tp0 == 1)
323 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);
327 fprintf(fplog, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec->nstlist, drmax);
335 fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax);
339 ngid = groups->grps[egcENER].nr;
340 gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
353 if (EEL_FULL(fr->eeltype))
358 snew(sum_UgembU, nener);
360 /* Initialize random generator */
361 tpi_rand = gmx_rng_init(inputrec->ld_seed);
365 fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
366 "TPI energies", "Time (ps)",
367 "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv);
368 xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
371 sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
372 leg[e++] = strdup(str);
373 sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
374 leg[e++] = strdup(str);
375 sprintf(str, "f. <e\\S-\\betaU\\N>");
376 leg[e++] = strdup(str);
377 sprintf(str, "f. V");
378 leg[e++] = strdup(str);
379 sprintf(str, "f. <Ue\\S-\\betaU\\N>");
380 leg[e++] = strdup(str);
381 for (i = 0; i < ngid; i++)
383 sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
384 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
385 leg[e++] = strdup(str);
389 sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
390 leg[e++] = strdup(str);
394 for (i = 0; i < ngid; i++)
396 sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
397 *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
398 leg[e++] = strdup(str);
402 sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
403 leg[e++] = strdup(str);
405 if (EEL_FULL(fr->eeltype))
407 sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
408 leg[e++] = strdup(str);
411 xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
412 for (i = 0; i < 4+nener; i++)
426 bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm),
427 &rerun_fr, TRX_NEED_X);
430 if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
431 mdatoms->nr - (a_tp1 - a_tp0))
433 gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s "
434 "is not equal the number in the run input file (%d) "
435 "minus the number of atoms to insert (%d)\n",
436 rerun_fr.natoms, bCavity ? " minus one" : "",
437 mdatoms->nr, a_tp1-a_tp0);
440 refvolshift = log(det(rerun_fr.box));
442 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
443 /* Make sure we don't detect SSE overflow generated before this point */
444 gmx_mm_check_and_reset_overflow();
447 while (bNotLastFrame)
449 lambda = rerun_fr.lambda;
453 for (e = 0; e < nener; e++)
458 /* Copy the coordinates from the input trajectory */
459 for (i = 0; i < rerun_fr.natoms; i++)
461 copy_rvec(rerun_fr.x[i], state->x[i]);
463 copy_mat(rerun_fr.box, state->box);
468 bStateChanged = TRUE;
470 for (step = 0; step < nsteps; step++)
472 /* In parallel all nodes generate all random configurations.
473 * In that way the result is identical to a single cpu tpi run.
477 /* Random insertion in the whole volume */
478 bNS = (step % inputrec->nstlist == 0);
481 /* Generate a random position in the box */
482 x_init[XX] = gmx_rng_uniform_real(tpi_rand)*state->box[XX][XX];
483 x_init[YY] = gmx_rng_uniform_real(tpi_rand)*state->box[YY][YY];
484 x_init[ZZ] = gmx_rng_uniform_real(tpi_rand)*state->box[ZZ][ZZ];
486 if (inputrec->nstlist == 1)
488 copy_rvec(x_init, x_tp);
492 /* Generate coordinates within |dx|=drmax of x_init */
495 dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
496 dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
497 dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
499 while (norm2(dx) > drmax*drmax);
500 rvec_add(x_init, dx, x_tp);
505 /* Random insertion around a cavity location
506 * given by the last coordinate of the trajectory.
512 /* Copy the location of the cavity */
513 copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init);
517 /* Determine the center of mass of the last molecule */
520 for (i = 0; i < nat_cavity; i++)
522 for (d = 0; d < DIM; d++)
525 mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
527 mass_tot += mass_cavity[i];
529 for (d = 0; d < DIM; d++)
531 x_init[d] /= mass_tot;
535 /* Generate coordinates within |dx|=drmax of x_init */
538 dx[XX] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
539 dx[YY] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
540 dx[ZZ] = (2*gmx_rng_uniform_real(tpi_rand) - 1)*drmax;
542 while (norm2(dx) > drmax*drmax);
543 rvec_add(x_init, dx, x_tp);
546 if (a_tp1 - a_tp0 == 1)
548 /* Insert a single atom, just copy the insertion location */
549 copy_rvec(x_tp, state->x[a_tp0]);
553 /* Copy the coordinates from the top file */
554 for (i = a_tp0; i < a_tp1; i++)
556 copy_rvec(x_mol[i-a_tp0], state->x[i]);
558 /* Rotate the molecule randomly */
559 rotate_conf(a_tp1-a_tp0, state->x+a_tp0, NULL,
560 2*M_PI*gmx_rng_uniform_real(tpi_rand),
561 2*M_PI*gmx_rng_uniform_real(tpi_rand),
562 2*M_PI*gmx_rng_uniform_real(tpi_rand));
563 /* Shift to the insertion location */
564 for (i = a_tp0; i < a_tp1; i++)
566 rvec_inc(state->x[i], x_tp);
570 /* Check if this insertion belongs to this node */
574 switch (inputrec->eI)
577 bOurStep = ((step / inputrec->nstlist) % nnodes == cr->nodeid);
580 bOurStep = (step % nnodes == cr->nodeid);
583 gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
588 /* Clear some matrix variables */
589 clear_mat(force_vir);
590 clear_mat(shake_vir);
594 /* Set the charge group center of mass of the test particle */
595 copy_rvec(x_init, fr->cg_cm[top->cgs.nr-1]);
597 /* Calc energy (no forces) on new positions.
598 * Since we only need the intermolecular energy
599 * and the RF exclusion terms of the inserted molecule occur
600 * within a single charge group we can pass NULL for the graph.
601 * This also avoids shifts that would move charge groups
604 * Some checks above ensure than we can not have
605 * twin-range interactions together with nstlist > 1,
606 * therefore we do not need to remember the LR energies.
608 /* Make do_force do a single node force calculation */
610 do_force(fplog, cr, inputrec,
611 step, nrnb, wcycle, top, &top_global->groups,
612 state->box, state->x, &state->hist,
613 f, force_vir, mdatoms, enerd, fcd,
615 NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE,
616 GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
617 (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) |
618 (bStateChanged ? GMX_FORCE_STATECHANGED : 0));
620 bStateChanged = FALSE;
623 /* Calculate long range corrections to pressure and energy */
624 calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
625 lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
626 /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
627 enerd->term[F_DISPCORR] = enercorr;
628 enerd->term[F_EPOT] += enercorr;
629 enerd->term[F_PRES] += prescorr;
630 enerd->term[F_DVDL_VDW] += dvdlcorr;
632 epot = enerd->term[F_EPOT];
633 bEnergyOutOfBounds = FALSE;
634 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
635 /* With SSE the energy can overflow, check for this */
636 if (gmx_mm_check_and_reset_overflow())
640 fprintf(debug, "Found an SSE overflow, assuming the energy is out of bounds\n");
642 bEnergyOutOfBounds = TRUE;
645 /* If the compiler doesn't optimize this check away
646 * we catch the NAN energies.
647 * The epot>GMX_REAL_MAX check catches inf values,
648 * which should nicely result in embU=0 through the exp below,
649 * but it does not hurt to check anyhow.
651 /* Non-bonded Interaction usually diverge at r=0.
652 * With tabulated interaction functions the first few entries
653 * should be capped in a consistent fashion between
654 * repulsion, dispersion and Coulomb to avoid accidental
655 * negative values in the total energy.
656 * The table generation code in tables.c does this.
657 * With user tbales the user should take care of this.
659 if (epot != epot || epot > GMX_REAL_MAX)
661 bEnergyOutOfBounds = TRUE;
663 if (bEnergyOutOfBounds)
667 fprintf(debug, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, step, epot);
673 embU = exp(-beta*epot);
675 /* Determine the weighted energy contributions of each energy group */
677 sum_UgembU[e++] += epot*embU;
680 for (i = 0; i < ngid; i++)
683 (enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] +
684 enerd->grpp.ener[egBHAMLR][GID(i, gid_tp, ngid)])*embU;
689 for (i = 0; i < ngid; i++)
692 (enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] +
693 enerd->grpp.ener[egLJLR][GID(i, gid_tp, ngid)])*embU;
698 sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
702 for (i = 0; i < ngid; i++)
705 (enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] +
706 enerd->grpp.ener[egCOULLR][GID(i, gid_tp, ngid)])*embU;
710 sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
712 if (EEL_FULL(fr->eeltype))
714 sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
719 if (embU == 0 || beta*epot > bU_bin_limit)
725 i = (int)((bU_logV_bin_limit
726 - (beta*epot - logV + refvolshift))*invbinw
734 realloc_bins(&bin, &nbin, i+10);
741 fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
742 step, epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
745 if (dump_pdb && epot <= dump_ener)
747 sprintf(str, "t%g_step%d.pdb", t, step);
748 sprintf(str2, "t: %f step %d ener: %f", t, step, epot);
749 write_sto_conf_mtop(str, str2, top_global, state->x, state->v,
750 inputrec->ePBC, state->box);
757 /* When running in parallel sum the energies over the processes */
758 gmx_sumd(1, &sum_embU, cr);
759 gmx_sumd(nener, sum_UgembU, cr);
764 VembU_all += V*sum_embU/nsteps;
768 if (bVerbose || frame%10 == 0 || frame < 10)
770 fprintf(stderr, "mu %10.3e <mu> %10.3e\n",
771 -log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta);
774 fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e",
776 VembU_all == 0 ? 20/beta : -log(VembU_all/V_all)/beta,
777 sum_embU == 0 ? 20/beta : -log(sum_embU/nsteps)/beta,
779 for (e = 0; e < nener; e++)
781 fprintf(fp_tpi, " %12.5e", sum_UgembU[e]/nsteps);
783 fprintf(fp_tpi, "\n");
787 bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
788 } /* End of the loop */
789 walltime_accounting_end(walltime_accounting);
795 gmx_fio_fclose(fp_tpi);
800 fprintf(fplog, "\n");
801 fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame);
802 fprintf(fplog, " <mu> = %12.5e kJ/mol\n", -log(VembU_all/V_all)/beta);
805 /* Write the Boltzmann factor histogram */
808 /* When running in parallel sum the bins over the processes */
811 realloc_bins(&bin, &nbin, i);
812 gmx_sumd(nbin, bin, cr);
816 fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
817 "TPI energy distribution",
818 "\\betaU - log(V/<V>)", "count", oenv);
819 sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
820 xvgr_subtitle(fp_tpi, str, oenv);
821 xvgr_legend(fp_tpi, 2, (const char **)tpid_leg, oenv);
822 for (i = nbin-1; i > 0; i--)
824 bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
825 fprintf(fp_tpi, "%6.2f %10d %12.5e\n",
828 bin[i]*exp(-bUlogV)*V_all/VembU_all);
830 gmx_fio_fclose(fp_tpi);
836 walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps);