double do_tpi(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact, int gmx_unused nstglobalcomm, gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr, int gmx_unused stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t gmx_unused ed, t_forcerec *fr, int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed, gmx_membed_t gmx_unused membed, real gmx_unused cpt_period, real gmx_unused max_hours, const char gmx_unused *deviceOptions, int gmx_unused imdport, unsigned long gmx_unused Flags, gmx_walltime_accounting_t walltime_accounting) { const char *TPI = "Test Particle Insertion"; gmx_localtop_t *top; gmx_groups_t *groups; gmx_enerdata_t *enerd; rvec *f; real lambda, t, temp, beta, drmax, epot; double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all; t_trxstatus *status; t_trxframe rerun_fr; gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS; tensor force_vir, shake_vir, vir, pres; int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e; rvec *x_mol; rvec mu_tot, x_init, dx, x_tp; int nnodes, frame; gmx_int64_t frame_step_prev, frame_step; gmx_int64_t nsteps, stepblocksize = 0, step; gmx_int64_t rnd_count_stride, rnd_count; gmx_int64_t seed; double rnd[4]; int i, start, end; FILE *fp_tpi = NULL; char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN]; double dbl, dump_ener; gmx_bool bCavity; int nat_cavity = 0, d; real *mass_cavity = NULL, mass_tot; int nbin; double invbinw, *bin, refvolshift, logV, bUlogV; real dvdl, prescorr, enercorr, dvdlcorr; gmx_bool bEnergyOutOfBounds; const char *tpid_leg[2] = {"direct", "reweighted"}; /* Since there is no upper limit to the insertion energies, * we need to set an upper limit for the distribution output. */ real bU_bin_limit = 50; real bU_logV_bin_limit = bU_bin_limit + 10; nnodes = cr->nnodes; top = gmx_mtop_generate_local_top(top_global, inputrec); groups = &top_global->groups; bCavity = (inputrec->eI == eiTPIC); if (bCavity) { ptr = getenv("GMX_TPIC_MASSES"); if (ptr == NULL) { nat_cavity = 1; } else { /* Read (multiple) masses from env var GMX_TPIC_MASSES, * The center of mass of the last atoms is then used for TPIC. */ nat_cavity = 0; while (sscanf(ptr, "%lf%n", &dbl, &i) > 0) { srenew(mass_cavity, nat_cavity+1); mass_cavity[nat_cavity] = dbl; fprintf(fplog, "mass[%d] = %f\n", nat_cavity+1, mass_cavity[nat_cavity]); nat_cavity++; ptr += i; } if (nat_cavity == 0) { gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity); } } } /* init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot, state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/ /* We never need full pbc for TPI */ fr->ePBC = epbcXYZ; /* Determine the temperature for the Boltzmann weighting */ temp = inputrec->opts.ref_t[0]; if (fplog) { for (i = 1; (i < inputrec->opts.ngtc); i++) { if (inputrec->opts.ref_t[i] != temp) { fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n"); fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n"); } } fprintf(fplog, "\n The temperature for test particle insertion is %.3f K\n\n", temp); } beta = 1.0/(BOLTZ*temp); /* Number of insertions per frame */ nsteps = inputrec->nsteps; /* Use the same neighborlist with more insertions points * in a sphere of radius drmax around the initial point */ /* This should be a proper mdp parameter */ drmax = inputrec->rtpi; /* An environment variable can be set to dump all configurations * to pdb with an insertion energy <= this value. */ dump_pdb = getenv("GMX_TPI_DUMP"); dump_ener = 0; if (dump_pdb) { sscanf(dump_pdb, "%lf", &dump_ener); } atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms); update_mdatoms(mdatoms, inputrec->fepvals->init_lambda); snew(enerd, 1); init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd); snew(f, top_global->natoms); /* Print to log file */ walltime_accounting_start(walltime_accounting); wallcycle_start(wcycle, ewcRUN); print_start(fplog, cr, walltime_accounting, "Test Particle Insertion"); /* The last charge group is the group to be inserted */ cg_tp = top->cgs.nr - 1; a_tp0 = top->cgs.index[cg_tp]; a_tp1 = top->cgs.index[cg_tp+1]; if (debug) { fprintf(debug, "TPI cg %d, atoms %d-%d\n", cg_tp, a_tp0, a_tp1); } if (a_tp1 - a_tp0 > 1 && (inputrec->rlist < inputrec->rcoulomb || inputrec->rlist < inputrec->rvdw)) { gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off"); } snew(x_mol, a_tp1-a_tp0); bDispCorr = (inputrec->eDispCorr != edispcNO); bCharge = FALSE; for (i = a_tp0; i < a_tp1; i++) { /* Copy the coordinates of the molecule to be insterted */ copy_rvec(state->x[i], x_mol[i-a_tp0]); /* Check if we need to print electrostatic energies */ bCharge |= (mdatoms->chargeA[i] != 0 || (mdatoms->chargeB && mdatoms->chargeB[i] != 0)); } bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype != eelRF_NEC); calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state->x, fr->cg_cm); if (bCavity) { if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog) { fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n"); fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n"); } } else { /* Center the molecule to be inserted at zero */ for (i = 0; i < a_tp1-a_tp0; i++) { rvec_dec(x_mol[i], fr->cg_cm[cg_tp]); } } if (fplog) { fprintf(fplog, "\nWill insert %d atoms %s partial charges\n", a_tp1-a_tp0, bCharge ? "with" : "without"); fprintf(fplog, "\nWill insert %d times in each frame of %s\n", (int)nsteps, opt2fn("-rerun", nfile, fnm)); } if (!bCavity) { if (inputrec->nstlist > 1) { if (drmax == 0 && a_tp1-a_tp0 == 1) { 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); } if (fplog) { fprintf(fplog, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec->nstlist, drmax); } } } else { if (fplog) { fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax); } } ngid = groups->grps[egcENER].nr; gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]); nener = 1 + ngid; if (bDispCorr) { nener += 1; } if (bCharge) { nener += ngid; if (bRFExcl) { nener += 1; } if (EEL_FULL(fr->eeltype)) { nener += 1; } } snew(sum_UgembU, nener); /* Copy the random seed set by the user */ seed = inputrec->ld_seed; /* We use the frame step number as one random counter. * The second counter use the insertion (step) count. But we * need multiple random numbers per insertion. This number is * not fixed, since we generate random locations in a sphere * by putting locations in a cube and some of these fail. * A count of 20 is already extremely unlikely, so 10000 is * a safe margin for random numbers per insertion. */ rnd_count_stride = 10000; if (MASTER(cr)) { fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm), "TPI energies", "Time (ps)", "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv); xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv); snew(leg, 4+nener); e = 0; sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)"); leg[e++] = strdup(str); sprintf(str, "f. -kT log<e\\S-\\betaU\\N>"); leg[e++] = strdup(str); sprintf(str, "f. <e\\S-\\betaU\\N>"); leg[e++] = strdup(str); sprintf(str, "f. V"); leg[e++] = strdup(str); sprintf(str, "f. <Ue\\S-\\betaU\\N>"); leg[e++] = strdup(str); for (i = 0; i < ngid; i++) { sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>", *(groups->grpname[groups->grps[egcENER].nm_ind[i]])); leg[e++] = strdup(str); } if (bDispCorr) { sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>"); leg[e++] = strdup(str); } if (bCharge) { for (i = 0; i < ngid; i++) { sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>", *(groups->grpname[groups->grps[egcENER].nm_ind[i]])); leg[e++] = strdup(str); } if (bRFExcl) { sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>"); leg[e++] = strdup(str); } if (EEL_FULL(fr->eeltype)) { sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>"); leg[e++] = strdup(str); } } xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv); for (i = 0; i < 4+nener; i++) { sfree(leg[i]); } sfree(leg); } clear_rvec(x_init); V_all = 0; VembU_all = 0; invbinw = 10; nbin = 10; snew(bin, nbin); /* Avoid frame step numbers <= -1 */ frame_step_prev = -1; bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X); frame = 0; if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) != mdatoms->nr - (a_tp1 - a_tp0)) { gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s " "is not equal the number in the run input file (%d) " "minus the number of atoms to insert (%d)\n", rerun_fr.natoms, bCavity ? " minus one" : "", mdatoms->nr, a_tp1-a_tp0); } refvolshift = log(det(rerun_fr.box)); switch (inputrec->eI) { case eiTPI: stepblocksize = inputrec->nstlist; break; case eiTPIC: stepblocksize = 1; break; default: gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]); } #ifdef GMX_SIMD /* Make sure we don't detect SIMD overflow generated before this point */ gmx_simd_check_and_reset_overflow(); #endif while (bNotLastFrame) { frame_step = rerun_fr.step; if (frame_step <= frame_step_prev) { /* We don't have step number in the trajectory file, * or we have constant or decreasing step numbers. * Ensure we have increasing step numbers, since we use * the step numbers as a counter for random numbers. */ frame_step = frame_step_prev + 1; } frame_step_prev = frame_step; lambda = rerun_fr.lambda; t = rerun_fr.time; sum_embU = 0; for (e = 0; e < nener; e++) { sum_UgembU[e] = 0; } /* Copy the coordinates from the input trajectory */ for (i = 0; i < rerun_fr.natoms; i++) { copy_rvec(rerun_fr.x[i], state->x[i]); } copy_mat(rerun_fr.box, state->box); V = det(state->box); logV = log(V); bStateChanged = TRUE; bNS = TRUE; step = cr->nodeid*stepblocksize; while (step < nsteps) { /* Initialize the second counter for random numbers using * the insertion step index. This ensures that we get * the same random numbers independently of how many * MPI ranks we use. Also for the same seed, we get * the same initial random sequence for different nsteps. */ rnd_count = step*rnd_count_stride; if (!bCavity) { /* Random insertion in the whole volume */ bNS = (step % inputrec->nstlist == 0); if (bNS) { /* Generate a random position in the box */ gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd); gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2); for (d = 0; d < DIM; d++) { x_init[d] = rnd[d]*state->box[d][d]; } } if (inputrec->nstlist == 1) { copy_rvec(x_init, x_tp); } else { /* Generate coordinates within |dx|=drmax of x_init */ do { gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd); gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2); for (d = 0; d < DIM; d++) { dx[d] = (2*rnd[d] - 1)*drmax; } } while (norm2(dx) > drmax*drmax); rvec_add(x_init, dx, x_tp); } } else { /* Random insertion around a cavity location * given by the last coordinate of the trajectory. */ if (step == 0) { if (nat_cavity == 1) { /* Copy the location of the cavity */ copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init); } else { /* Determine the center of mass of the last molecule */ clear_rvec(x_init); mass_tot = 0; for (i = 0; i < nat_cavity; i++) { for (d = 0; d < DIM; d++) { x_init[d] += mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d]; } mass_tot += mass_cavity[i]; } for (d = 0; d < DIM; d++) { x_init[d] /= mass_tot; } } } /* Generate coordinates within |dx|=drmax of x_init */ do { gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd); gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2); for (d = 0; d < DIM; d++) { dx[d] = (2*rnd[d] - 1)*drmax; } } while (norm2(dx) > drmax*drmax); rvec_add(x_init, dx, x_tp); } if (a_tp1 - a_tp0 == 1) { /* Insert a single atom, just copy the insertion location */ copy_rvec(x_tp, state->x[a_tp0]); } else { /* Copy the coordinates from the top file */ for (i = a_tp0; i < a_tp1; i++) { copy_rvec(x_mol[i-a_tp0], state->x[i]); } /* Rotate the molecule randomly */ gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd); gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2); rotate_conf(a_tp1-a_tp0, state->x+a_tp0, NULL, 2*M_PI*rnd[0], 2*M_PI*rnd[1], 2*M_PI*rnd[2]); /* Shift to the insertion location */ for (i = a_tp0; i < a_tp1; i++) { rvec_inc(state->x[i], x_tp); } } /* Clear some matrix variables */ clear_mat(force_vir); clear_mat(shake_vir); clear_mat(vir); clear_mat(pres); /* Set the charge group center of mass of the test particle */ copy_rvec(x_init, fr->cg_cm[top->cgs.nr-1]); /* Calc energy (no forces) on new positions. * Since we only need the intermolecular energy * and the RF exclusion terms of the inserted molecule occur * within a single charge group we can pass NULL for the graph. * This also avoids shifts that would move charge groups * out of the box. * * Some checks above ensure than we can not have * twin-range interactions together with nstlist > 1, * therefore we do not need to remember the LR energies. */ /* Make do_force do a single node force calculation */ cr->nnodes = 1; do_force(fplog, cr, inputrec, step, nrnb, wcycle, top, &top_global->groups, state->box, state->x, &state->hist, f, force_vir, mdatoms, enerd, fcd, state->lambda, NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE, GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) | (bStateChanged ? GMX_FORCE_STATECHANGED : 0)); cr->nnodes = nnodes; bStateChanged = FALSE; bNS = FALSE; /* Calculate long range corrections to pressure and energy */ calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box, lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr); /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */ enerd->term[F_DISPCORR] = enercorr; enerd->term[F_EPOT] += enercorr; enerd->term[F_PRES] += prescorr; enerd->term[F_DVDL_VDW] += dvdlcorr; epot = enerd->term[F_EPOT]; bEnergyOutOfBounds = FALSE; #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER /* With SSE the energy can overflow, check for this */ if (gmx_mm_check_and_reset_overflow()) { if (debug) { fprintf(debug, "Found an SSE overflow, assuming the energy is out of bounds\n"); } bEnergyOutOfBounds = TRUE; } #endif /* If the compiler doesn't optimize this check away * we catch the NAN energies. * The epot>GMX_REAL_MAX check catches inf values, * which should nicely result in embU=0 through the exp below, * but it does not hurt to check anyhow. */ /* Non-bonded Interaction usually diverge at r=0. * With tabulated interaction functions the first few entries * should be capped in a consistent fashion between * repulsion, dispersion and Coulomb to avoid accidental * negative values in the total energy. * The table generation code in tables.c does this. * With user tbales the user should take care of this. */ if (epot != epot || epot > GMX_REAL_MAX) { bEnergyOutOfBounds = TRUE; } if (bEnergyOutOfBounds) { if (debug) { fprintf(debug, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, (int)step, epot); } embU = 0; } else { embU = exp(-beta*epot); sum_embU += embU; /* Determine the weighted energy contributions of each energy group */ e = 0; sum_UgembU[e++] += epot*embU; if (fr->bBHAM) { for (i = 0; i < ngid; i++) { sum_UgembU[e++] += (enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] + enerd->grpp.ener[egBHAMLR][GID(i, gid_tp, ngid)])*embU; } } else { for (i = 0; i < ngid; i++) { sum_UgembU[e++] += (enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] + enerd->grpp.ener[egLJLR][GID(i, gid_tp, ngid)])*embU; } } if (bDispCorr) { sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU; } if (bCharge) { for (i = 0; i < ngid; i++) { sum_UgembU[e++] += (enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] + enerd->grpp.ener[egCOULLR][GID(i, gid_tp, ngid)])*embU; } if (bRFExcl) { sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU; } if (EEL_FULL(fr->eeltype)) { sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU; } } } if (embU == 0 || beta*epot > bU_bin_limit) { bin[0]++; } else { i = (int)((bU_logV_bin_limit - (beta*epot - logV + refvolshift))*invbinw + 0.5); if (i < 0) { i = 0; } if (i >= nbin) { realloc_bins(&bin, &nbin, i+10); } bin[i]++; } if (debug) { fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n", (int)step, epot, x_tp[XX], x_tp[YY], x_tp[ZZ]); } if (dump_pdb && epot <= dump_ener) { sprintf(str, "t%g_step%d.pdb", t, (int)step); sprintf(str2, "t: %f step %d ener: %f", t, (int)step, epot); write_sto_conf_mtop(str, str2, top_global, state->x, state->v, inputrec->ePBC, state->box); } step++; if ((step/stepblocksize) % cr->nnodes != cr->nodeid) { /* Skip all steps assigned to the other MPI ranks */ step += (cr->nnodes - 1)*stepblocksize; } } if (PAR(cr)) { /* When running in parallel sum the energies over the processes */ gmx_sumd(1, &sum_embU, cr); gmx_sumd(nener, sum_UgembU, cr); } frame++; V_all += V; VembU_all += V*sum_embU/nsteps; if (fp_tpi) { if (bVerbose || frame%10 == 0 || frame < 10) { fprintf(stderr, "mu %10.3e <mu> %10.3e\n", -log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta); } fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e", t, VembU_all == 0 ? 20/beta : -log(VembU_all/V_all)/beta, sum_embU == 0 ? 20/beta : -log(sum_embU/nsteps)/beta, sum_embU/nsteps, V); for (e = 0; e < nener; e++) { fprintf(fp_tpi, " %12.5e", sum_UgembU[e]/nsteps); } fprintf(fp_tpi, "\n"); fflush(fp_tpi); } bNotLastFrame = read_next_frame(oenv, status, &rerun_fr); } /* End of the loop */ walltime_accounting_end(walltime_accounting); close_trj(status); if (fp_tpi != NULL) { gmx_fio_fclose(fp_tpi); } if (fplog != NULL) { fprintf(fplog, "\n"); fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame); fprintf(fplog, " <mu> = %12.5e kJ/mol\n", -log(VembU_all/V_all)/beta); } /* Write the Boltzmann factor histogram */ if (PAR(cr)) { /* When running in parallel sum the bins over the processes */ i = nbin; global_max(cr, &i); realloc_bins(&bin, &nbin, i); gmx_sumd(nbin, bin, cr); } if (MASTER(cr)) { fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm), "TPI energy distribution", "\\betaU - log(V/<V>)", "count", oenv); sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]); xvgr_subtitle(fp_tpi, str, oenv); xvgr_legend(fp_tpi, 2, (const char **)tpid_leg, oenv); for (i = nbin-1; i > 0; i--) { bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame); fprintf(fp_tpi, "%6.2f %10d %12.5e\n", bUlogV, (int)(bin[i]+0.5), bin[i]*exp(-bUlogV)*V_all/VembU_all); } gmx_fio_fclose(fp_tpi); } sfree(bin); sfree(sum_UgembU); walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps); return 0; }
static void test_for_replica_exchange(FILE *fplog, const gmx_multisim_t *ms, struct gmx_repl_ex *re, gmx_enerdata_t *enerd, real vol, gmx_int64_t step, real time) { int m, i, j, a, b, ap, bp, i0, i1, tmp; real ediff = 0, delta = 0, dpV = 0; gmx_bool bPrint, bMultiEx; gmx_bool *bEx = re->bEx; real *prob = re->prob; int *pind = re->destinations; /* permuted index */ gmx_bool bEpot = FALSE; gmx_bool bDLambda = FALSE; gmx_bool bVol = FALSE; gmx_rng_t rng; bMultiEx = (re->nex > 1); /* multiple exchanges at each state */ fprintf(fplog, "Replica exchange at step " "%"GMX_PRId64 " time %g\n", step, time); if (re->bNPT) { for (i = 0; i < re->nrepl; i++) { re->Vol[i] = 0; } bVol = TRUE; re->Vol[re->repl] = vol; } if ((re->type == ereTEMP || re->type == ereTL)) { for (i = 0; i < re->nrepl; i++) { re->Epot[i] = 0; } bEpot = TRUE; re->Epot[re->repl] = enerd->term[F_EPOT]; /* temperatures of different states*/ for (i = 0; i < re->nrepl; i++) { re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ); } } else { for (i = 0; i < re->nrepl; i++) { re->beta[i] = 1.0/(re->temp*BOLTZ); /* we have a single temperature */ } } if (re->type == ereLAMBDA || re->type == ereTL) { bDLambda = TRUE; /* lambda differences. */ /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian minus the energy of the jth simulation in the jth Hamiltonian */ for (i = 0; i < re->nrepl; i++) { for (j = 0; j < re->nrepl; j++) { re->de[i][j] = 0; } } for (i = 0; i < re->nrepl; i++) { re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]); } } /* now actually do the communication */ if (bVol) { gmx_sum_sim(re->nrepl, re->Vol, ms); } if (bEpot) { gmx_sum_sim(re->nrepl, re->Epot, ms); } if (bDLambda) { for (i = 0; i < re->nrepl; i++) { gmx_sum_sim(re->nrepl, re->de[i], ms); } } /* make a duplicate set of indices for shuffling */ for (i = 0; i < re->nrepl; i++) { pind[i] = re->ind[i]; } if (bMultiEx) { /* multiple random switch exchange */ int nself = 0; for (i = 0; i < re->nex + nself; i++) { double rnd[2]; gmx_rng_cycle_2uniform(step, i*2, re->seed, RND_SEED_REPLEX, rnd); /* randomly select a pair */ /* in theory, could reduce this by identifying only which switches had a nonneglibible probability of occurring (log p > -100) and only operate on those switches */ /* find out which state it is from, and what label that state currently has. Likely more work that useful. */ i0 = (int)(re->nrepl*rnd[0]); i1 = (int)(re->nrepl*rnd[1]); if (i0 == i1) { nself++; continue; /* self-exchange, back up and do it again */ } a = re->ind[i0]; /* what are the indices of these states? */ b = re->ind[i1]; ap = pind[i0]; bp = pind[i1]; bPrint = FALSE; /* too noisy */ /* calculate the energy difference */ /* if the code changes to flip the STATES, rather than the configurations, use the commented version of the code */ /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */ delta = calc_delta(fplog, bPrint, re, ap, bp, a, b); /* we actually only use the first space in the prob and bEx array, since there are actually many switches between pairs. */ if (delta <= 0) { /* accepted */ prob[0] = 1; bEx[0] = TRUE; } else { if (delta > PROBABILITYCUTOFF) { prob[0] = 0; } else { prob[0] = exp(-delta); } /* roll a number to determine if accepted */ gmx_rng_cycle_2uniform(step, i*2+1, re->seed, RND_SEED_REPLEX, rnd); bEx[0] = rnd[0] < prob[0]; } re->prob_sum[0] += prob[0]; if (bEx[0]) { /* swap the states */ tmp = pind[i0]; pind[i0] = pind[i1]; pind[i1] = tmp; } } re->nattempt[0]++; /* keep track of total permutation trials here */ print_allswitchind(fplog, re->nrepl, pind, re->allswaps, re->tmpswap); } else { /* standard nearest neighbor replica exchange */ m = (step / re->nst) % 2; for (i = 1; i < re->nrepl; i++) { a = re->ind[i-1]; b = re->ind[i]; bPrint = (re->repl == a || re->repl == b); if (i % 2 == m) { delta = calc_delta(fplog, bPrint, re, a, b, a, b); if (delta <= 0) { /* accepted */ prob[i] = 1; bEx[i] = TRUE; } else { double rnd[2]; if (delta > PROBABILITYCUTOFF) { prob[i] = 0; } else { prob[i] = exp(-delta); } /* roll a number to determine if accepted */ gmx_rng_cycle_2uniform(step, i, re->seed, RND_SEED_REPLEX, rnd); bEx[i] = rnd[0] < prob[i]; } re->prob_sum[i] += prob[i]; if (bEx[i]) { /* swap these two */ tmp = pind[i-1]; pind[i-1] = pind[i]; pind[i] = tmp; re->nexchange[i]++; /* statistics for back compatibility */ } } else { prob[i] = -1; bEx[i] = FALSE; } } /* print some statistics */ print_ind(fplog, "ex", re->nrepl, re->ind, bEx); print_prob(fplog, "pr", re->nrepl, prob); fprintf(fplog, "\n"); re->nattempt[m]++; } /* record which moves were made and accepted */ for (i = 0; i < re->nrepl; i++) { re->nmoves[re->ind[i]][pind[i]] += 1; re->nmoves[pind[i]][re->ind[i]] += 1; } fflush(fplog); /* make sure we can see what the last exchange was */ }
static int ChooseNewLambda(int nlim, t_expanded *expand, df_history_t *dfhist, int fep_state, real *weighted_lamee, double *p_k, gmx_int64_t seed, gmx_int64_t step) { /* Choose new lambda value, and update transition matrix */ int i, ifep, minfep, maxfep, lamnew, lamtrial, starting_fep_state; real r1, r2, de, trialprob, tprob = 0; double *propose, *accept, *remainder; double pks; real pnorm; starting_fep_state = fep_state; lamnew = fep_state; /* so that there is a default setting -- stays the same */ if (!EWL(expand->elamstats)) /* ignore equilibrating the weights if using WL */ { if ((expand->lmc_forced_nstart > 0) && (dfhist->n_at_lam[nlim-1] <= expand->lmc_forced_nstart)) { /* Use a marching method to run through the lambdas and get preliminary free energy data, before starting 'free' sampling. We start free sampling when we have enough at each lambda */ /* if we have enough at this lambda, move on to the next one */ if (dfhist->n_at_lam[fep_state] == expand->lmc_forced_nstart) { lamnew = fep_state+1; if (lamnew == nlim) /* whoops, stepped too far! */ { lamnew -= 1; } } else { lamnew = fep_state; } return lamnew; } } snew(propose, nlim); snew(accept, nlim); snew(remainder, nlim); for (i = 0; i < expand->lmc_repeats; i++) { double rnd[2]; gmx_rng_cycle_2uniform(step, i, seed, RND_SEED_EXPANDED, rnd); for (ifep = 0; ifep < nlim; ifep++) { propose[ifep] = 0; accept[ifep] = 0; } if ((expand->elmcmove == elmcmoveGIBBS) || (expand->elmcmove == elmcmoveMETGIBBS)) { /* use the Gibbs sampler, with restricted range */ if (expand->gibbsdeltalam < 0) { minfep = 0; maxfep = nlim-1; } else { minfep = fep_state - expand->gibbsdeltalam; maxfep = fep_state + expand->gibbsdeltalam; if (minfep < 0) { minfep = 0; } if (maxfep > nlim-1) { maxfep = nlim-1; } } GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, minfep, maxfep); if (expand->elmcmove == elmcmoveGIBBS) { for (ifep = minfep; ifep <= maxfep; ifep++) { propose[ifep] = p_k[ifep]; accept[ifep] = 1.0; } /* Gibbs sampling */ r1 = rnd[0]; for (lamnew = minfep; lamnew <= maxfep; lamnew++) { if (r1 <= p_k[lamnew]) { break; } r1 -= p_k[lamnew]; } } else if (expand->elmcmove == elmcmoveMETGIBBS) { /* Metropolized Gibbs sampling */ for (ifep = minfep; ifep <= maxfep; ifep++) { remainder[ifep] = 1 - p_k[ifep]; } /* find the proposal probabilities */ if (remainder[fep_state] == 0) { /* only the current state has any probability */ /* we have to stay at the current state */ lamnew = fep_state; } else { for (ifep = minfep; ifep <= maxfep; ifep++) { if (ifep != fep_state) { propose[ifep] = p_k[ifep]/remainder[fep_state]; } else { propose[ifep] = 0; } } r1 = rnd[0]; for (lamtrial = minfep; lamtrial <= maxfep; lamtrial++) { pnorm = p_k[lamtrial]/remainder[fep_state]; if (lamtrial != fep_state) { if (r1 <= pnorm) { break; } r1 -= pnorm; } } /* we have now selected lamtrial according to p(lamtrial)/1-p(fep_state) */ tprob = 1.0; /* trial probability is min{1,\frac{1 - p(old)}{1-p(new)} MRS 1/8/2008 */ trialprob = (remainder[fep_state])/(remainder[lamtrial]); if (trialprob < tprob) { tprob = trialprob; } r2 = rnd[1]; if (r2 < tprob) { lamnew = lamtrial; } else { lamnew = fep_state; } } /* now figure out the acceptance probability for each */ for (ifep = minfep; ifep <= maxfep; ifep++) { tprob = 1.0; if (remainder[ifep] != 0) { trialprob = (remainder[fep_state])/(remainder[ifep]); } else { trialprob = 1.0; /* this state is the only choice! */ } if (trialprob < tprob) { tprob = trialprob; } /* probability for fep_state=0, but that's fine, it's never proposed! */ accept[ifep] = tprob; } } if (lamnew > maxfep) { /* it's possible some rounding is failing */ if (gmx_within_tol(remainder[fep_state], 0, 50*GMX_DOUBLE_EPS)) { /* numerical rounding error -- no state other than the original has weight */ lamnew = fep_state; } else { /* probably not a numerical issue */ int loc = 0; int nerror = 200+(maxfep-minfep+1)*60; char *errorstr; snew(errorstr, nerror); /* if its greater than maxfep, then something went wrong -- probably underflow in the calculation of sum weights. Generated detailed info for failure */ loc += sprintf(errorstr, "Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination.\nDenominator is: %3d%17.10e\n i dE numerator weights\n", 0, pks); for (ifep = minfep; ifep <= maxfep; ifep++) { loc += sprintf(&errorstr[loc], "%3d %17.10e%17.10e%17.10e\n", ifep, weighted_lamee[ifep], p_k[ifep], dfhist->sum_weights[ifep]); } gmx_fatal(FARGS, errorstr); } } } else if ((expand->elmcmove == elmcmoveMETROPOLIS) || (expand->elmcmove == elmcmoveBARKER)) { /* use the metropolis sampler with trial +/- 1 */ r1 = rnd[0]; if (r1 < 0.5) { if (fep_state == 0) { lamtrial = fep_state; } else { lamtrial = fep_state-1; } } else { if (fep_state == nlim-1) { lamtrial = fep_state; } else { lamtrial = fep_state+1; } } de = weighted_lamee[lamtrial] - weighted_lamee[fep_state]; if (expand->elmcmove == elmcmoveMETROPOLIS) { tprob = 1.0; trialprob = std::exp(de); if (trialprob < tprob) { tprob = trialprob; } propose[fep_state] = 0; propose[lamtrial] = 1.0; /* note that this overwrites the above line if fep_state = ntrial, which only occurs at the ends */ accept[fep_state] = 1.0; /* doesn't actually matter, never proposed unless fep_state = ntrial, in which case it's 1.0 anyway */ accept[lamtrial] = tprob; } else if (expand->elmcmove == elmcmoveBARKER) { tprob = 1.0/(1.0+std::exp(-de)); propose[fep_state] = (1-tprob); propose[lamtrial] += tprob; /* we add, to account for the fact that at the end, they might be the same point */ accept[fep_state] = 1.0; accept[lamtrial] = 1.0; } r2 = rnd[1]; if (r2 < tprob) { lamnew = lamtrial; } else { lamnew = fep_state; } } for (ifep = 0; ifep < nlim; ifep++) { dfhist->Tij[fep_state][ifep] += propose[ifep]*accept[ifep]; dfhist->Tij[fep_state][fep_state] += propose[ifep]*(1.0-accept[ifep]); } fep_state = lamnew; } dfhist->Tij_empirical[starting_fep_state][lamnew] += 1.0; sfree(propose); sfree(accept); sfree(remainder); return lamnew; }