From: Erik Lindahl Date: Sun, 22 Jun 2014 14:15:09 +0000 (+0200) Subject: Make log file option listing similar to mdp names X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=dbf38ec430054a717d5bcc504d27f2f0827e664d;p=alexxy%2Fgromacs.git Make log file option listing similar to mdp names Modify names to be consistent with the mdp file spelling and abbreviations, to the extent possible. This patch also removes the unused ndelta option. Fixes #1514. Change-Id: I3e56ee3dc773d027b2c0c5ca060fa34e4930a4d6 --- diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c index c5ee1e2e71..f8db1c8a89 100644 --- a/src/gromacs/fileio/tpxio.c +++ b/src/gromacs/fileio/tpxio.c @@ -923,7 +923,7 @@ static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead, } gmx_fio_do_int(fio, ir->ns_type); gmx_fio_do_int(fio, ir->nstlist); - gmx_fio_do_int(fio, ir->ndelta); + gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */ if (file_version < 41) { gmx_fio_do_int(fio, idum); diff --git a/src/gromacs/gmxlib/txtdump.c b/src/gromacs/gmxlib/txtdump.c index 47876e9591..6450a7c3f9 100644 --- a/src/gromacs/gmxlib/txtdump.c +++ b/src/gromacs/gmxlib/txtdump.c @@ -448,11 +448,11 @@ void pr_qm_opts(FILE *fp, int indent, const char *title, t_grpopts *opts) pr_ivec(fp, indent, "QMbasis", opts->QMbasis, opts->ngQM, FALSE); pr_ivec(fp, indent, "QMcharge", opts->QMcharge, opts->ngQM, FALSE); pr_ivec(fp, indent, "QMmult", opts->QMmult, opts->ngQM, FALSE); - pr_bvec(fp, indent, "bSH", opts->bSH, opts->ngQM, FALSE); + pr_bvec(fp, indent, "SH", opts->bSH, opts->ngQM, FALSE); pr_ivec(fp, indent, "CASorbitals", opts->CASorbitals, opts->ngQM, FALSE); pr_ivec(fp, indent, "CASelectrons", opts->CASelectrons, opts->ngQM, FALSE); pr_rvec(fp, indent, "SAon", opts->SAon, opts->ngQM, FALSE); - pr_rvec(fp, indent, "SAon", opts->SAon, opts->ngQM, FALSE); + pr_rvec(fp, indent, "SAoff", opts->SAoff, opts->ngQM, FALSE); pr_ivec(fp, indent, "SAsteps", opts->SAsteps, opts->ngQM, FALSE); pr_bvec(fp, indent, "bOPT", opts->bOPT, opts->ngQM, FALSE); pr_bvec(fp, indent, "bTS", opts->bTS, opts->ngQM, FALSE); @@ -494,14 +494,14 @@ static void pr_grp_opts(FILE *out, int indent, const char *title, t_grpopts *opt fprintf(out, "\n"); /* Pretty-print the simulated annealing info */ - fprintf(out, "anneal%s", bMDPformat ? " = " : ":"); + fprintf(out, "annealing%s", bMDPformat ? " = " : ":"); for (i = 0; (i < opts->ngtc); i++) { fprintf(out, " %10s", EANNEAL(opts->annealing[i])); } fprintf(out, "\n"); - fprintf(out, "ann-npoints%s", bMDPformat ? " = " : ":"); + fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":"); for (i = 0; (i < opts->ngtc); i++) { fprintf(out, " %10d", opts->anneal_npoints[i]); @@ -512,13 +512,13 @@ static void pr_grp_opts(FILE *out, int indent, const char *title, t_grpopts *opt { if (opts->anneal_npoints[i] > 0) { - fprintf(out, "ann. times [%d]:\t", i); + fprintf(out, "annealing-time [%d]:\t", i); for (j = 0; (j < opts->anneal_npoints[i]); j++) { fprintf(out, " %10.1f", opts->anneal_time[i][j]); } fprintf(out, "\n"); - fprintf(out, "ann. temps [%d]:\t", i); + fprintf(out, "annealing-temp [%d]:\t", i); for (j = 0; (j < opts->anneal_npoints[i]); j++) { fprintf(out, " %10.1f", opts->anneal_temp[i][j]); @@ -644,9 +644,9 @@ static void pr_pull_coord(FILE *fp, int indent, int c, t_pull_coord *pcrd) static void pr_simtempvals(FILE *fp, int indent, t_simtemp *simtemp, int n_lambda) { - PR("simtemp_low", simtemp->simtemp_low); - PR("simtemp_high", simtemp->simtemp_high); PS("simulated-tempering-scaling", ESIMTEMP(simtemp->eSimTempScale)); + PR("sim-temp-low", simtemp->simtemp_low); + PR("sim-temp-high", simtemp->simtemp_high); pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures, n_lambda, TRUE); } @@ -654,21 +654,8 @@ static void pr_expandedvals(FILE *fp, int indent, t_expanded *expand, int n_lamb { PI("nstexpanded", expand->nstexpanded); - PS("lambda-stats", elamstats_names[expand->elamstats]); - PS("lambda-mc-move", elmcmove_names[expand->elmcmove]); - PI("lmc-repeats", expand->lmc_repeats); - PI("lmc-gibbsdelta", expand->gibbsdeltalam); - PI("lmc-nstart", expand->lmc_forced_nstart); - PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix)); - PI("nst-transition-matrix", expand->nstTij); - PI("mininum-var-min", expand->minvarmin); /*default is reasonable */ - PI("weight-c-range", expand->c_range); /* default is just C=0 */ - PR("wl-scale", expand->wl_scale); - PR("init-wl-delta", expand->init_wl_delta); - PR("wl-ratio", expand->wl_ratio); - PS("bWLoneovert", EBOOL(expand->bWLoneovert)); - PI("lmc-seed", expand->lmc_seed); - PR("mc-temperature", expand->mc_temp); + PS("lmc-stats", elamstats_names[expand->elamstats]); + PS("lmc-move", elmcmove_names[expand->elmcmove]); PS("lmc-weights-equil", elmceq_names[expand->elmceq]); if (expand->elmceq == elmceqNUMATLAM) { @@ -690,6 +677,19 @@ static void pr_expandedvals(FILE *fp, int indent, t_expanded *expand, int n_lamb { PR("weight-equil-count-ratio", expand->equil_ratio); } + PI("lmc-seed", expand->lmc_seed); + PR("mc-temperature", expand->mc_temp); + PI("lmc-repeats", expand->lmc_repeats); + PI("lmc-gibbsdelta", expand->gibbsdeltalam); + PI("lmc-forced-nstart", expand->lmc_forced_nstart); + PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix)); + PI("nst-transition-matrix", expand->nstTij); + PI("mininum-var-min", expand->minvarmin); /*default is reasonable */ + PI("weight-c-range", expand->c_range); /* default is just C=0 */ + PR("wl-scale", expand->wl_scale); + PR("wl-ratio", expand->wl_ratio); + PR("init-wl-delta", expand->init_wl_delta); + PS("wl-oneovert", EBOOL(expand->bWLoneovert)); pr_indent(fp, indent); pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights, n_lambda, TRUE); @@ -700,10 +700,11 @@ static void pr_fepvals(FILE *fp, int indent, t_lambda *fep, gmx_bool bMDPformat) { int i, j; - PI("nstdhdl", fep->nstdhdl); - PI("init-lambda-state", fep->init_fep_state); PR("init-lambda", fep->init_lambda); + PI("init-lambda-state", fep->init_fep_state); PR("delta-lambda", fep->delta_lambda); + PI("nstdhdl", fep->nstdhdl); + if (!bMDPformat) { PI("n-lambdas", fep->n_lambda); @@ -737,18 +738,17 @@ static void pr_fepvals(FILE *fp, int indent, t_lambda *fep, gmx_bool bMDPformat) } } PI("calc-lambda-neighbors", fep->lambda_neighbors); - + PS("dhdl-print-energy", EBOOL(fep->bPrintEnergy)); PR("sc-alpha", fep->sc_alpha); - PS("bScCoul", EBOOL(fep->bScCoul)); - PS("bScPrintEnergy", EBOOL(fep->bPrintEnergy)); PI("sc-power", fep->sc_power); PR("sc-r-power", fep->sc_r_power); PR("sc-sigma", fep->sc_sigma); PR("sc-sigma-min", fep->sc_sigma_min); - PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file)); - PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives)); + PS("sc-coul", EBOOL(fep->bScCoul)); PI("dh-hist-size", fep->dh_hist_size); PD("dh-hist-spacing", fep->dh_hist_spacing); + PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file)); + PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives)); }; static void pr_pull(FILE *fp, int indent, t_pull *pull) @@ -760,15 +760,15 @@ static void pr_pull(FILE *fp, int indent, t_pull *pull) PR("pull-r1", pull->cyl_r1); PR("pull-r0", pull->cyl_r0); PR("pull-constr-tol", pull->constr_tol); - PS("pull-bPrintRef", EBOOL(pull->bPrintRef)); + PS("pull-print-reference", EBOOL(pull->bPrintRef)); PI("pull-nstxout", pull->nstxout); PI("pull-nstfout", pull->nstfout); - PI("pull-ngroup", pull->ngroup); + PI("pull-ngroups", pull->ngroup); for (g = 0; g < pull->ngroup; g++) { pr_pull_group(fp, indent, g, &pull->group[g]); } - PI("pull-ncoord", pull->ncoord); + PI("pull-ncoords", pull->ncoord); for (g = 0; g < pull->ncoord; g++) { pr_pull_coord(fp, indent, g, &pull->coord[g]); @@ -778,31 +778,31 @@ static void pr_pull(FILE *fp, int indent, t_pull *pull) static void pr_rotgrp(FILE *fp, int indent, int g, t_rotgrp *rotg) { pr_indent(fp, indent); - fprintf(fp, "rotation_group %d:\n", g); + fprintf(fp, "rot-group %d:\n", g); indent += 2; - PS("type", EROTGEOM(rotg->eType)); - PS("massw", EBOOL(rotg->bMassW)); + PS("rot-type", EROTGEOM(rotg->eType)); + PS("rot-massw", EBOOL(rotg->bMassW)); pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE); - pr_rvecs(fp, indent, "x_ref", rotg->x_ref, rotg->nat); - pr_rvec(fp, indent, "vec", rotg->vec, DIM, TRUE); - pr_rvec(fp, indent, "pivot", rotg->pivot, DIM, TRUE); - PR("rate", rotg->rate); - PR("k", rotg->k); - PR("slab_dist", rotg->slab_dist); - PR("min_gaussian", rotg->min_gaussian); - PR("epsilon", rotg->eps); - PS("fit_method", EROTFIT(rotg->eFittype)); - PI("potfitangle_nstep", rotg->PotAngle_nstep); - PR("potfitangle_step", rotg->PotAngle_step); + pr_rvecs(fp, indent, "x-ref", rotg->x_ref, rotg->nat); + pr_rvec(fp, indent, "rot-vec", rotg->vec, DIM, TRUE); + pr_rvec(fp, indent, "rot-pivot", rotg->pivot, DIM, TRUE); + PR("rot-rate", rotg->rate); + PR("rot-k", rotg->k); + PR("rot-slab-dist", rotg->slab_dist); + PR("rot-min-gauss", rotg->min_gaussian); + PR("rot-eps", rotg->eps); + PS("rot-fit-method", EROTFIT(rotg->eFittype)); + PI("rot_potfit_nstep", rotg->PotAngle_nstep); + PR("rot_potfit_step", rotg->PotAngle_step); } static void pr_rot(FILE *fp, int indent, t_rot *rot) { int g; - PI("rot_nstrout", rot->nstrout); - PI("rot_nstsout", rot->nstsout); - PI("rot_ngrp", rot->ngrp); + PI("rot-nstrout", rot->nstrout); + PI("rot-nstsout", rot->nstsout); + PI("rot-ngroups", rot->ngrp); for (g = 0; g < rot->ngrp; g++) { pr_rotgrp(fp, indent, g, &rot->grp[g]); @@ -816,37 +816,37 @@ static void pr_swap(FILE *fp, int indent, t_swapcoords *swap) char str[STRLEN]; - PI("frequency", swap->nstswap); - for (j = 0; j < 2; j++) - { - sprintf(str, "nanions%c", j+'A'); - PI(str, swap->nanions[j]); - sprintf(str, "ncations%c", j+'A'); - PI(str, swap->ncations[j]); - } - PI("coupling_steps", swap->nAverage); - PR("threshold", swap->threshold); + PI("swap-frequency", swap->nstswap); for (j = 0; j < 2; j++) { - sprintf(str, "splitgroup%d_massw", j); + sprintf(str, "massw_split%d", j); PS(str, EBOOL(swap->massw_split[j])); sprintf(str, "split atoms group %d", j); pr_ivec_block(fp, indent, str, swap->ind_split[j], swap->nat_split[j], TRUE); } pr_ivec_block(fp, indent, "swap atoms", swap->ind, swap->nat, TRUE); pr_ivec_block(fp, indent, "solvent atoms", swap->ind_sol, swap->nat_sol, TRUE); - PR("cyl0_radius", swap->cyl0r); - PR("cyl0_upper", swap->cyl0u); - PR("cyl0_lower", swap->cyl0l); - PR("cyl1_radius", swap->cyl1r); - PR("cyl1_upper", swap->cyl1u); - PR("cyl1_lower", swap->cyl1l); + PR("cyl0-r", swap->cyl0r); + PR("cyl0-up", swap->cyl0u); + PR("cyl0-down", swap->cyl0l); + PR("cyl1-r", swap->cyl1r); + PR("cyl1-up", swap->cyl1u); + PR("cyl1-down", swap->cyl1l); + PI("coupl-steps", swap->nAverage); + for (j = 0; j < 2; j++) + { + sprintf(str, "anions%c", j+'A'); + PI(str, swap->nanions[j]); + sprintf(str, "cations%c", j+'A'); + PI(str, swap->ncations[j]); + } + PR("threshold", swap->threshold); } static void pr_imd(FILE *fp, int indent, t_IMD *imd) { - PI("IMD_atoms", imd->nat); + PI("IMD-atoms", imd->nat); pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE); } @@ -863,84 +863,60 @@ void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir, { indent = pr_title(fp, indent, title); } - /* This strings do not all have a direct correspondence to - .mdp entries, but we should follow the same convention of - using hyphens in the names users read and write. */ + /* Try to make this list appear in the same order as the + * options are written in the default mdout.mdp, and with + * the same user-exposed names to facilitate debugging. + */ PS("integrator", EI(ir->eI)); + PR("tinit", ir->init_t); + PR("dt", ir->delta_t); PSTEP("nsteps", ir->nsteps); PSTEP("init-step", ir->init_step); - PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme)); - PS("ns-type", ENS(ir->ns_type)); - PI("nstlist", ir->nstlist); - PI("ndelta", ir->ndelta); - PI("nstcomm", ir->nstcomm); + PI("simulation-part", ir->simulation_part); PS("comm-mode", ECOM(ir->comm_mode)); - PI("nstlog", ir->nstlog); + PI("nstcomm", ir->nstcomm); + + /* Langevin dynamics */ + PR("bd-fric", ir->bd_fric); + PSTEP("ld-seed", ir->ld_seed); + + /* Energy minimization */ + PR("emtol", ir->em_tol); + PR("emstep", ir->em_stepsize); + PI("niter", ir->niter); + PR("fcstep", ir->fc_stepsize); + PI("nstcgsteep", ir->nstcgsteep); + PI("nbfgscorr", ir->nbfgscorr); + + /* Test particle insertion */ + PR("rtpi", ir->rtpi); + + /* Output control */ PI("nstxout", ir->nstxout); PI("nstvout", ir->nstvout); PI("nstfout", ir->nstfout); + PI("nstlog", ir->nstlog); PI("nstcalcenergy", ir->nstcalcenergy); PI("nstenergy", ir->nstenergy); PI("nstxout-compressed", ir->nstxout_compressed); - PR("init-t", ir->init_t); - PR("delta-t", ir->delta_t); + PR("compressed-x-precision", ir->x_compression_precision); - PR("x-compression-precision", ir->x_compression_precision); - PR("fourierspacing", ir->fourier_spacing); - PI("nkx", ir->nkx); - PI("nky", ir->nky); - PI("nkz", ir->nkz); - PI("pme-order", ir->pme_order); - PR("ewald-rtol", ir->ewald_rtol); - PR("ewald-rtol-lj", ir->ewald_rtol_lj); - PR("ewald-geometry", ir->ewald_geometry); - PR("epsilon-surface", ir->epsilon_surface); - PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule)); - PS("ePBC", EPBC(ir->ePBC)); - PS("bPeriodicMols", EBOOL(ir->bPeriodicMols)); - PS("bContinuation", EBOOL(ir->bContinuation)); - PS("bShakeSOR", EBOOL(ir->bShakeSOR)); - PS("etc", ETCOUPLTYPE(ir->etc)); - PS("bPrintNHChains", EBOOL(ir->bPrintNHChains)); - PI("nsttcouple", ir->nsttcouple); - PS("epc", EPCOUPLTYPE(ir->epc)); - PS("epctype", EPCOUPLTYPETYPE(ir->epct)); - PI("nstpcouple", ir->nstpcouple); - PR("tau-p", ir->tau_p); - pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat); - pr_matrix(fp, indent, "compress", ir->compress, bMDPformat); - PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling)); - if (bMDPformat) - { - fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], - ir->posres_com[YY], ir->posres_com[ZZ]); - } - else - { - pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM, TRUE); - } - if (bMDPformat) - { - fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], - ir->posres_comB[YY], ir->posres_comB[ZZ]); - } - else - { - pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM, TRUE); - } + /* Neighborsearching parameters */ + PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme)); + PI("nstlist", ir->nstlist); + PS("ns-type", ENS(ir->ns_type)); + PS("pbc", EPBC(ir->ePBC)); + PS("periodic-molecules", EBOOL(ir->bPeriodicMols)); PR("verlet-buffer-tolerance", ir->verletbuf_tol); PR("rlist", ir->rlist); PR("rlistlong", ir->rlistlong); PR("nstcalclr", ir->nstcalclr); - PR("rtpi", ir->rtpi); + + /* Options for electrostatics and VdW */ PS("coulombtype", EELTYPE(ir->coulombtype)); PS("coulomb-modifier", INTMODIFIER(ir->coulomb_modifier)); PR("rcoulomb-switch", ir->rcoulomb_switch); PR("rcoulomb", ir->rcoulomb); - PS("vdwtype", EVDWTYPE(ir->vdwtype)); - PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier)); - PR("rvdw-switch", ir->rvdw_switch); - PR("rvdw", ir->rvdw); if (ir->epsilon_r != 0) { PR("epsilon-r", ir->epsilon_r); @@ -957,12 +933,32 @@ void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir, { PS("epsilon-rf", infbuf); } - PR("tabext", ir->tabext); + PS("vdw-type", EVDWTYPE(ir->vdwtype)); + PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier)); + PR("rvdw-switch", ir->rvdw_switch); + PR("rvdw", ir->rvdw); + PS("DispCorr", EDISPCORR(ir->eDispCorr)); + PR("table-extension", ir->tabext); + + PR("fourierspacing", ir->fourier_spacing); + PI("fourier-nx", ir->nkx); + PI("fourier-ny", ir->nky); + PI("fourier-nz", ir->nkz); + PI("pme-order", ir->pme_order); + PR("ewald-rtol", ir->ewald_rtol); + PR("ewald-rtol-lj", ir->ewald_rtol_lj); + PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule)); + PR("ewald-geometry", ir->ewald_geometry); + PR("epsilon-surface", ir->epsilon_surface); + + /* Implicit solvent */ PS("implicit-solvent", EIMPLICITSOL(ir->implicit_solvent)); + + /* Generalized born electrostatics */ PS("gb-algorithm", EGBALGORITHM(ir->gb_algorithm)); - PR("gb-epsilon-solvent", ir->gb_epsilon_solvent); PI("nstgbradii", ir->nstgbradii); PR("rgbradii", ir->rgbradii); + PR("gb-epsilon-solvent", ir->gb_epsilon_solvent); PR("gb-saltconc", ir->gb_saltconc); PR("gb-obc-alpha", ir->gb_obc_alpha); PR("gb-obc-beta", ir->gb_obc_beta); @@ -970,75 +966,134 @@ void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir, PR("gb-dielectric-offset", ir->gb_dielectric_offset); PS("sa-algorithm", ESAALGORITHM(ir->gb_algorithm)); PR("sa-surface-tension", ir->sa_surface_tension); - PS("DispCorr", EDISPCORR(ir->eDispCorr)); - PS("bSimTemp", EBOOL(ir->bSimTemp)); - if (ir->bSimTemp) - { - pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda); - } - PS("free-energy", EFEPTYPE(ir->efep)); - if (ir->efep != efepNO || ir->bSimTemp) + + /* Options for weak coupling algorithms */ + PS("tcoupl", ETCOUPLTYPE(ir->etc)); + PI("nsttcouple", ir->nsttcouple); + PI("nh-chain-length", ir->opts.nhchainlength); + PS("print-nose-hoover-chain-variables", EBOOL(ir->bPrintNHChains)); + + PS("pcoupl", EPCOUPLTYPE(ir->epc)); + PS("pcoupltype", EPCOUPLTYPETYPE(ir->epct)); + PI("nstpcouple", ir->nstpcouple); + PR("tau-p", ir->tau_p); + pr_matrix(fp, indent, "compressibility", ir->compress, bMDPformat); + pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat); + PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling)); + + if (bMDPformat) { - pr_fepvals(fp, indent, ir->fepvals, bMDPformat); + fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], + ir->posres_com[YY], ir->posres_com[ZZ]); + fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], + ir->posres_comB[YY], ir->posres_comB[ZZ]); } - if (ir->bExpanded) + else { - pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda); + pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM, TRUE); + pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM, TRUE); } + /* QMMM */ + PS("QMMM", EBOOL(ir->bQMMM)); + PI("QMconstraints", ir->QMconstraints); + PI("QMMMscheme", ir->QMMMscheme); + PR("MMChargeScaleFactor", ir->scalefactor); + pr_qm_opts(fp, indent, "qm-opts", &(ir->opts)); + + /* CONSTRAINT OPTIONS */ + PS("constraint-algorithm", ECONSTRTYPE(ir->eConstrAlg)); + PS("continuation", EBOOL(ir->bContinuation)); + + PS("Shake-SOR", EBOOL(ir->bShakeSOR)); + PR("shake-tol", ir->shake_tol); + PI("lincs-order", ir->nProjOrder); + PI("lincs-iter", ir->nLincsIter); + PR("lincs-warnangle", ir->LincsWarnAngle); + + /* Walls */ PI("nwall", ir->nwall); PS("wall-type", EWALLTYPE(ir->wall_type)); + PR("wall-r-linpot", ir->wall_r_linpot); + /* wall-atomtype */ PI("wall-atomtype[0]", ir->wall_atomtype[0]); PI("wall-atomtype[1]", ir->wall_atomtype[1]); + /* wall-density */ PR("wall-density[0]", ir->wall_density[0]); PR("wall-density[1]", ir->wall_density[1]); PR("wall-ewald-zfac", ir->wall_ewald_zfac); + /* COM PULLING */ PS("pull", EPULLTYPE(ir->ePull)); if (ir->ePull != epullNO) { pr_pull(fp, indent, ir->pull); } + /* ENFORCED ROTATION */ PS("rotation", EBOOL(ir->bRot)); if (ir->bRot) { pr_rot(fp, indent, ir->rot); } + /* INTERACTIVE MD */ PS("interactiveMD", EBOOL(ir->bIMD)); if (ir->bIMD) { pr_imd(fp, indent, ir->imd); } + /* NMR refinement stuff */ PS("disre", EDISRETYPE(ir->eDisre)); PS("disre-weighting", EDISREWEIGHTING(ir->eDisreWeighting)); PS("disre-mixed", EBOOL(ir->bDisreMixed)); PR("dr-fc", ir->dr_fc); PR("dr-tau", ir->dr_tau); PR("nstdisreout", ir->nstdisreout); - PR("orires-fc", ir->orires_fc); - PR("orires-tau", ir->orires_tau); + + PR("orire-fc", ir->orires_fc); + PR("orire-tau", ir->orires_tau); PR("nstorireout", ir->nstorireout); - PR("em-stepsize", ir->em_stepsize); - PR("em-tol", ir->em_tol); - PI("niter", ir->niter); - PR("fc-stepsize", ir->fc_stepsize); - PI("nstcgsteep", ir->nstcgsteep); - PI("nbfgscorr", ir->nbfgscorr); + /* FREE ENERGY VARIABLES */ + PS("free-energy", EFEPTYPE(ir->efep)); + if (ir->efep != efepNO || ir->bSimTemp) + { + pr_fepvals(fp, indent, ir->fepvals, bMDPformat); + } + if (ir->bExpanded) + { + pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda); + } - PS("ConstAlg", ECONSTRTYPE(ir->eConstrAlg)); - PR("shake-tol", ir->shake_tol); - PI("lincs-order", ir->nProjOrder); - PR("lincs-warnangle", ir->LincsWarnAngle); - PI("lincs-iter", ir->nLincsIter); - PR("bd-fric", ir->bd_fric); - PSTEP("ld-seed", ir->ld_seed); - PR("cos-accel", ir->cos_accel); + /* NON-equilibrium MD stuff */ + PR("cos-acceleration", ir->cos_accel); pr_matrix(fp, indent, "deform", ir->deform, bMDPformat); + /* SIMULATED TEMPERING */ + PS("simulated-tempering", EBOOL(ir->bSimTemp)); + if (ir->bSimTemp) + { + pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda); + } + + /* ELECTRIC FIELDS */ + pr_cosine(fp, indent, "E-x", &(ir->ex[XX]), bMDPformat); + pr_cosine(fp, indent, "E-xt", &(ir->et[XX]), bMDPformat); + pr_cosine(fp, indent, "E-y", &(ir->ex[YY]), bMDPformat); + pr_cosine(fp, indent, "E-yt", &(ir->et[YY]), bMDPformat); + pr_cosine(fp, indent, "E-z", &(ir->ex[ZZ]), bMDPformat); + pr_cosine(fp, indent, "E-zt", &(ir->et[ZZ]), bMDPformat); + + /* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */ + PS("swapcoords", ESWAPTYPE(ir->eSwapCoords)); + if (ir->eSwapCoords != eswapNO) + { + pr_swap(fp, indent, ir->swap); + } + + /* AdResS PARAMETERS */ PS("adress", EBOOL(ir->bAdress)); if (ir->bAdress) { @@ -1046,13 +1101,14 @@ void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir, PR("adress-const-wf", ir->adress->const_wf); PR("adress-ex-width", ir->adress->ex_width); PR("adress-hy-width", ir->adress->hy_width); + PR("adress-ex-forcecap", ir->adress->ex_forcecap); PS("adress-interface-correction", EADRESSICTYPE(ir->adress->icor)); PS("adress-site", EADRESSSITETYPE(ir->adress->site)); - PR("adress-ex-force-cap", ir->adress->ex_forcecap); - PS("adress-do-hybridpairs", EBOOL(ir->adress->do_hybridpairs)); - pr_rvec(fp, indent, "adress-reference-coords", ir->adress->refs, DIM, TRUE); + PS("adress-do-hybridpairs", EBOOL(ir->adress->do_hybridpairs)); } + + /* USER-DEFINED THINGIES */ PI("userint1", ir->userint1); PI("userint2", ir->userint2); PI("userint3", ir->userint3); @@ -1061,23 +1117,8 @@ void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir, PR("userreal2", ir->userreal2); PR("userreal3", ir->userreal3); PR("userreal4", ir->userreal4); + pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat); - pr_cosine(fp, indent, "efield-x", &(ir->ex[XX]), bMDPformat); - pr_cosine(fp, indent, "efield-xt", &(ir->et[XX]), bMDPformat); - pr_cosine(fp, indent, "efield-y", &(ir->ex[YY]), bMDPformat); - pr_cosine(fp, indent, "efield-yt", &(ir->et[YY]), bMDPformat); - pr_cosine(fp, indent, "efield-z", &(ir->ex[ZZ]), bMDPformat); - pr_cosine(fp, indent, "efield-zt", &(ir->et[ZZ]), bMDPformat); - PS("eSwapCoords", ESWAPTYPE(ir->eSwapCoords)); - if (ir->eSwapCoords != eswapNO) - { - pr_swap(fp, indent, ir->swap); - } - PS("bQMMM", EBOOL(ir->bQMMM)); - PI("QMconstraints", ir->QMconstraints); - PI("QMMMscheme", ir->QMMMscheme); - PR("scalefactor", ir->scalefactor); - pr_qm_opts(fp, indent, "qm-opts", &(ir->opts)); } } #undef PS diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c index 27a3b5b752..64f1f2853e 100644 --- a/src/gromacs/gmxpreprocess/addconf.c +++ b/src/gromacs/gmxpreprocess/addconf.c @@ -260,7 +260,6 @@ static void do_nsgrid(FILE *fp, gmx_bool bVerbose, ir->vdw_modifier = eintmodNONE; ir->coulombtype = eelCUT; ir->vdwtype = evdwCUT; - ir->ndelta = 2; ir->ns_type = ensGRID; snew(ir->opts.egp_flags, 1); diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c index a2f84972f2..3c3b99f172 100644 --- a/src/gromacs/gmxpreprocess/readir.c +++ b/src/gromacs/gmxpreprocess/readir.c @@ -1866,8 +1866,6 @@ void get_ir(const char *mdparin, const char *mdparout, ITYPE ("nstlist", ir->nstlist, 10); CTYPE ("ns algorithm (simple or grid)"); EETYPE("ns-type", ir->ns_type, ens_names); - /* set ndelta to the optimal value of 2 */ - ir->ndelta = 2; CTYPE ("Periodic boundary conditions: xyz, no, xy"); EETYPE("pbc", ir->ePBC, epbc_names); EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names); diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c index c23aa35668..9f8b5769bc 100644 --- a/src/gromacs/gmxpreprocess/readpull.c +++ b/src/gromacs/gmxpreprocess/readpull.c @@ -149,7 +149,7 @@ char **read_pullparams(int *ninp_p, t_inpfile **inp_p, RTYPE("pull-r1", pull->cyl_r1, 1.0); CTYPE("Switch from r1 to r0 in case of dynamic reaction force"); RTYPE("pull-r0", pull->cyl_r0, 1.5); - RTYPE("pull_constr_tol", pull->constr_tol, 1E-6); + RTYPE("pull-constr-tol", pull->constr_tol, 1E-6); EETYPE("pull-start", *bStart, yesno_names); EETYPE("pull-print-reference", pull->bPrintRef, yesno_names); ITYPE("pull-nstxout", pull->nstxout, 10); diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c index 1f3a2348a9..fd22977925 100644 --- a/src/gromacs/tools/compare.c +++ b/src/gromacs/tools/compare.c @@ -753,7 +753,6 @@ static void cmp_inputrec(FILE *fp, t_inputrec *ir1, t_inputrec *ir2, real ftol, cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme); cmp_int(fp, "inputrec->ns_type", -1, ir1->ns_type, ir2->ns_type); cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist); - cmp_int(fp, "inputrec->ndelta", -1, ir1->ndelta, ir2->ndelta); cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm); cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode); cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);