* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/* This file is completely threadsafe - please keep it that way! */
+#include "gromacs/legacyheaders/txtdump.h"
+
#include <stdio.h>
-#include "smalloc.h"
-#include "typedefs.h"
-#include "names.h"
-#include "txtdump.h"
-#include "string2.h"
-#include "vec.h"
-#include "macros.h"
+#include <stdlib.h>
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
int pr_indent(FILE *fp, int n)
{
const char *format;
int i, j;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
const char *format;
int i, j;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
const char *flong = "%15.8e";
const char *format;
- if (getenv("LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
{
format = flong;
}
static void pr_int(FILE *fp, int indent, const char *title, int i)
{
pr_indent(fp, indent);
- fprintf(fp, "%-20s = %d\n", title, i);
+ fprintf(fp, "%-30s = %d\n", title, i);
}
static void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i)
char buf[STEPSTRSIZE];
pr_indent(fp, indent);
- fprintf(fp, "%-20s = %s\n", title, gmx_step_str(i, buf));
+ fprintf(fp, "%-30s = %s\n", title, gmx_step_str(i, buf));
}
static void pr_real(FILE *fp, int indent, const char *title, real r)
{
pr_indent(fp, indent);
- fprintf(fp, "%-20s = %g\n", title, r);
+ fprintf(fp, "%-30s = %g\n", title, r);
}
static void pr_double(FILE *fp, int indent, const char *title, double d)
{
pr_indent(fp, indent);
- fprintf(fp, "%-20s = %g\n", title, d);
+ fprintf(fp, "%-30s = %g\n", title, d);
}
static void pr_str(FILE *fp, int indent, const char *title, const char *s)
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);
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]);
{
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]);
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);
}
{
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)
{
{
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);
{
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);
}
}
PI("calc-lambda-neighbors", fep->lambda_neighbors);
-
+ PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
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)
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]);
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]);
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);
+ pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
}
{
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("optimize-fft", EBOOL(ir->bOptFFT));
- 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);
{
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);
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("nstorireout", ir->nstorireout);
- PR("dihre-fc", ir->dihre_fc);
+ 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);
- PI("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)
{
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);
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
case F_CMAP:
fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
break;
+ case F_RESTRANGLES:
+ pr_harm(fp, iparams, "ktheta", "costheta0");
+ break;
+ case F_RESTRDIHS:
+ fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
+ iparams->pdihs.phiA, iparams->pdihs.cpA);
+ break;
+ case F_CBTDIHS:
+ fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
+ for (i = 1; i < NR_CBTDIHS; i++)
+ {
+ fprintf(fp, ", cbtcA[%d]=%15.8e", i-1, iparams->cbtdihs.cbtcA[i]);
+ }
+ fprintf(fp, "\n");
+ break;
default:
gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
ftype, interaction_function[ftype].name, __FILE__, __LINE__);
for (i = 0; i <= block->nr; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->index[%d]=%u\n",
+ (void) fprintf(fp, "%s->index[%d]=%d\n",
title, bShowNumbers ? i : -1, block->index[i]);
}
for (i = 0; i < block->nra; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->a[%d]=%u\n",
+ (void) fprintf(fp, "%s->a[%d]=%d\n",
title, bShowNumbers ? i : -1, block->a[i]);
}
}
(void) fprintf(fp, "\n");
size = pr_indent(fp, indent+INDENT);
}
- size += fprintf(fp, "%u", block->a[j]);
+ size += fprintf(fp, "%d", block->a[j]);
}
(void) fprintf(fp, "}\n");
start = end;
fprintf(fp, "commrec:\n");
indent += 2;
pr_indent(fp, indent);
- fprintf(fp, "nodeid = %d\n", cr->nodeid);
+ fprintf(fp, "rank = %d\n", cr->nodeid);
pr_indent(fp, indent);
- fprintf(fp, "nnodes = %d\n", cr->nnodes);
+ fprintf(fp, "number of ranks = %d\n", cr->nnodes);
pr_indent(fp, indent);
- fprintf(fp, "npmenodes = %d\n", cr->npmenodes);
+ fprintf(fp, "PME-only ranks = %d\n", cr->npmenodes);
/*
pr_indent(fp,indent);
fprintf(fp,"threadid = %d\n",cr->threadid);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff