void AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */) { if (!impl_->filename_.empty()) { if (impl_->bPlain_) { impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w"); } else { time_unit_t time_unit = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1); xvg_format_t xvg_format = (impl_->settings_.plotFormat() > 0 ? static_cast<xvg_format_t>(impl_->settings_.plotFormat()) : exvgNONE); output_env_t oenv; output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0); boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done); impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(), impl_->xlabel_.c_str(), impl_->ylabel_.c_str(), oenv); const SelectionCollection *selections = impl_->settings_.selectionCollection(); if (selections != NULL) { selections->printXvgrInfo(impl_->fp_, oenv); } if (!impl_->subtitle_.empty()) { xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv); } if (output_env_get_print_xvgr_codes(oenv) && !impl_->legend_.empty()) { std::vector<const char *> legend; legend.reserve(impl_->legend_.size()); for (size_t i = 0; i < impl_->legend_.size(); ++i) { legend.push_back(impl_->legend_[i].c_str()); } xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv); } } } }
extern FILE *open_dhdl(const char *filename, const t_inputrec *ir, const gmx_output_env_t *oenv) { FILE *fp; const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda", *lambdastate = "\\lambda state"; char title[STRLEN], label_x[STRLEN], label_y[STRLEN]; int i, nps, nsets, nsets_de, nsetsbegin; int n_lambda_terms = 0; t_lambda *fep = ir->fepvals; /* for simplicity */ t_expanded *expand = ir->expandedvals; char **setname; char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN]; int bufplace = 0; int nsets_dhdl = 0; int s = 0; int nsetsextend; gmx_bool write_pV = FALSE; /* count the number of different lambda terms */ for (i = 0; i < efptNR; i++) { if (fep->separate_dvdl[i]) { n_lambda_terms++; } } if (fep->n_lambda == 0) { sprintf(title, "%s", dhdl); sprintf(label_x, "Time (ps)"); sprintf(label_y, "%s (%s %s)", dhdl, unit_energy, "[\\lambda]\\S-1\\N"); } else { sprintf(title, "%s and %s", dhdl, deltag); sprintf(label_x, "Time (ps)"); sprintf(label_y, "%s and %s (%s %s)", dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N"); } fp = gmx_fio_fopen(filename, "w+"); xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv); if (!(ir->bSimTemp)) { bufplace = sprintf(buf, "T = %g (K) ", ir->opts.ref_t[0]); } if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED)) { if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 )) { /* compatibility output */ sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda); } else { print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE, lambda_vec_str); print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE, lambda_name_str); sprintf(&(buf[bufplace]), "%s %d: %s = %s", lambdastate, fep->init_fep_state, lambda_name_str, lambda_vec_str); } } xvgr_subtitle(fp, buf, oenv); nsets_dhdl = 0; if (fep->dhdl_derivatives == edhdlderivativesYES) { nsets_dhdl = n_lambda_terms; } /* count the number of delta_g states */ nsets_de = fep->lambda_stop_n - fep->lambda_start_n; nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */ if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO)) { nsets += 1; /*add fep state for expanded ensemble */ } if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO) { nsets += 1; /* add energy to the dhdl as well */ } nsetsextend = nsets; if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0)) { nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda, and only output when init_lambda is not set in order to maintain compatibility of the dhdl.xvg file) */ write_pV = TRUE; } snew(setname, nsetsextend); if (expand->elmcmove > elmcmoveNO) { /* state for the fep_vals, if we have alchemical sampling */ sprintf(buf, "%s", "Thermodynamic state"); setname[s] = gmx_strdup(buf); s += 1; } if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO) { switch (fep->edHdLPrintEnergy) { case edHdLPrintEnergyPOTENTIAL: sprintf(buf, "%s (%s)", "Potential Energy", unit_energy); break; case edHdLPrintEnergyTOTAL: case edHdLPrintEnergyYES: default: sprintf(buf, "%s (%s)", "Total Energy", unit_energy); } setname[s] = gmx_strdup(buf); s += 1; } if (fep->dhdl_derivatives == edhdlderivativesYES) { for (i = 0; i < efptNR; i++) { if (fep->separate_dvdl[i]) { if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 )) { /* compatibility output */ sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda); } else { double lam = fep->init_lambda; if (fep->init_lambda < 0) { lam = fep->all_lambda[i][fep->init_fep_state]; } sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i], lam); } setname[s] = gmx_strdup(buf); s += 1; } } } if (fep->n_lambda > 0) { /* g_bar has to determine the lambda values used in this simulation * from this xvg legend. */ if (expand->elmcmove > elmcmoveNO) { nsetsbegin = 1; /* for including the expanded ensemble */ } else { nsetsbegin = 0; } if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO) { nsetsbegin += 1; } nsetsbegin += nsets_dhdl; for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++) { print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str); if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 )) { /* for compatible dhdl.xvg files */ nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str); } else { nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str); } if (ir->bSimTemp) { /* print the temperature for this state if doing simulated annealing */ sprintf(&buf[nps], "T = %g (%s)", ir->simtempvals->temperatures[s-(nsetsbegin)], unit_temp_K); } setname[s] = gmx_strdup(buf); s++; } if (write_pV) { sprintf(buf, "pV (%s)", unit_energy); setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after nsets */ } xvgr_legend(fp, nsetsextend, (const char **)setname, oenv); for (s = 0; s < nsetsextend; s++) { sfree(setname[s]); } sfree(setname); } return fp; }
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; }
FILE *open_dhdl(const char *filename,const t_inputrec *ir, const output_env_t oenv) { FILE *fp; const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda"; char title[STRLEN],label_x[STRLEN],label_y[STRLEN]; char **setname; char buf[STRLEN]; sprintf(label_x,"%s (%s)","Time",unit_time); if (ir->n_flambda == 0) { sprintf(title,"%s",dhdl); sprintf(label_y,"%s (%s %s)", dhdl,unit_energy,"[\\lambda]\\S-1\\N"); } else { sprintf(title,"%s, %s",dhdl,deltag); sprintf(label_y,"(%s)",unit_energy); } fp = gmx_fio_fopen(filename,"w+"); xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv); if (ir->delta_lambda == 0) { sprintf(buf,"T = %g (K), %s = %g", ir->opts.ref_t[0],lambda,ir->init_lambda); } else { sprintf(buf,"T = %g (K)", ir->opts.ref_t[0]); } xvgr_subtitle(fp,buf,oenv); if (ir->n_flambda > 0) { int nsets,s,nsi=0; /* g_bar has to determine the lambda values used in this simulation * from this xvg legend. */ nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) + ir->n_flambda; snew(setname,nsets); if (ir->dhdl_derivatives == dhdlderivativesYES) { sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda); setname[nsi++] = strdup(buf); } for(s=0; s<ir->n_flambda; s++) { sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]); setname[nsi++] = strdup(buf); } xvgr_legend(fp,nsets,(const char**)setname,oenv); for(s=0; s<nsets; s++) { sfree(setname[s]); } sfree(setname); } return fp; }
extern FILE *open_dhdl(const char *filename,const t_inputrec *ir, const output_env_t oenv) { FILE *fp; const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda", *lambdastate="\\lambda state",*remain="remaining"; char title[STRLEN],label_x[STRLEN],label_y[STRLEN]; int i,np,nps,nsets,nsets_de,nsetsbegin; t_lambda *fep; char **setname; char buf[STRLEN]; int bufplace=0; int nsets_dhdl = 0; int s = 0; int nsetsextend; /* for simplicity */ fep = ir->fepvals; if (fep->n_lambda == 0) { sprintf(title,"%s",dhdl); sprintf(label_x,"Time (ps)"); sprintf(label_y,"%s (%s %s)", dhdl,unit_energy,"[\\lambda]\\S-1\\N"); } else { sprintf(title,"%s and %s",dhdl,deltag); sprintf(label_x,"Time (ps)"); sprintf(label_y,"%s and %s (%s %s)", dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N"); } fp = gmx_fio_fopen(filename,"w+"); xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv); if (!(ir->bSimTemp)) { bufplace = sprintf(buf,"T = %g (K) ", ir->opts.ref_t[0]); } if (ir->efep != efepSLOWGROWTH) { if (fep->n_lambda == 0) { sprintf(&(buf[bufplace]),"%s = %g", lambda,fep->init_lambda); } else { sprintf(&(buf[bufplace]),"%s = %d", lambdastate,fep->init_fep_state); } } xvgr_subtitle(fp,buf,oenv); for (i=0;i<efptNR;i++) { if (fep->separate_dvdl[i]) {nsets_dhdl++;} } /* count the number of delta_g states */ nsets_de = fep->n_lambda; nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */ if (fep->n_lambda>0 && ir->bExpanded) { nsets += 1; /*add fep state for expanded ensemble */ } if (fep->bPrintEnergy) { nsets += 1; /* add energy to the dhdl as well */ } nsetsextend = nsets; if ((ir->epc!=epcNO) && (fep->n_lambda>0)) { nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */ } snew(setname,nsetsextend); if (ir->bExpanded) { /* state for the fep_vals, if we have alchemical sampling */ sprintf(buf,"%s","Thermodynamic state"); setname[s] = strdup(buf); s+=1; } if (fep->bPrintEnergy) { sprintf(buf,"%s (%s)","Energy",unit_energy); setname[s] = strdup(buf); s+=1; } for (i=0;i<efptNR;i++) { if (fep->separate_dvdl[i]) { sprintf(buf,"%s (%s)",dhdl,efpt_names[i]); setname[s] = strdup(buf); s+=1; } } if (fep->n_lambda > 0) { /* g_bar has to determine the lambda values used in this simulation * from this xvg legend. */ if (ir->bExpanded) { nsetsbegin = 1; /* for including the expanded ensemble */ } else { nsetsbegin = 0; } if (fep->bPrintEnergy) { nsetsbegin += 1; } nsetsbegin += nsets_dhdl; for(s=nsetsbegin; s<nsets; s++) { nps = sprintf(buf,"%s %s (",deltag,lambda); for (i=0;i<efptNR;i++) { if (fep->separate_dvdl[i]) { np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]); nps += np; } } if (ir->bSimTemp) { /* print the temperature for this state if doing simulated annealing */ sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K); } else { sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */ } setname[s] = strdup(buf); } if (ir->epc!=epcNO) { np = sprintf(buf,"pV (%s)",unit_energy); setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */ } xvgr_legend(fp,nsetsextend,(const char **)setname,oenv); for(s=0; s<nsetsextend; s++) { sfree(setname[s]); } sfree(setname); } return fp; }