topology -> gmxlib
pbcutil -> fileio
pbcutil -> gmxlib
+pbcutil -> mdtypes
listed-forces -> mdlib
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio-xdr.h"
#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/fileio/xdr_datatype.h"
#include "gromacs/fileio/xdrf.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/sysinfo.h"
+#include "gromacs/utility/txtdump.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio-xdr.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/ifunc.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
#define TPX_TAG_RELEASE "release"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-/* This file is completely threadsafe - please keep it that way! */
-
-#include "txtdump.h"
-
-#include <cstdio>
-#include <cstdlib>
-
-#include "gromacs/math/vec.h"
-#include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/snprintf.h"
-#include "gromacs/utility/stringutil.h"
-
-//! Macro to select a bool name
-#define EBOOL(e) gmx::boolToString(e)
-
-int pr_indent(FILE *fp, int n)
-{
- int i;
-
- for (i = 0; i < n; i++)
- {
- fprintf(fp, " ");
- }
- return n;
-}
-
-int available(FILE *fp, const void *p, int indent, const char *title)
-{
- if (!p)
- {
- if (indent > 0)
- {
- pr_indent(fp, indent);
- }
- fprintf(fp, "%s: not available\n", title);
- }
- return (p != NULL);
-}
-
-int pr_title(FILE *fp, int indent, const char *title)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%s:\n", title);
- return (indent+INDENT);
-}
-
-int pr_title_n(FILE *fp, int indent, const char *title, int n)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%s (%d):\n", title, n);
- return (indent+INDENT);
-}
-
-int pr_title_nxn(FILE *fp, int indent, const char *title, int n1, int n2)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%s (%dx%d):\n", title, n1, n2);
- return (indent+INDENT);
-}
-
-void pr_ivec(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%d\n", title, bShowNumbers ? i : -1, vec[i]);
- }
- }
-}
-
-void pr_ivec_block(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers)
-{
- int i, j;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- i = 0;
- while (i < n)
- {
- j = i+1;
- while (j < n && vec[j] == vec[j-1]+1)
- {
- j++;
- }
- /* Print consecutive groups of 3 or more as blocks */
- if (j - i < 3)
- {
- while (i < j)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%d\n",
- title, bShowNumbers ? i : -1, vec[i]);
- i++;
- }
- }
- else
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d,...,%d] = {%d,...,%d}\n",
- title,
- bShowNumbers ? i : -1,
- bShowNumbers ? j-1 : -1,
- vec[i], vec[j-1]);
- i = j;
- }
- }
- }
-}
-
-void pr_bvec(FILE *fp, int indent, const char *title, const gmx_bool vec[], int n, gmx_bool bShowNumbers)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%s\n", title, bShowNumbers ? i : -1,
- EBOOL(vec[i]));
- }
- }
-}
-
-void pr_ivecs(FILE *fp, int indent, const char *title, const ivec vec[], int n, gmx_bool bShowNumbers)
-{
- int i, j;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_nxn(fp, indent, title, n, DIM);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]={", title, bShowNumbers ? i : -1);
- for (j = 0; j < DIM; j++)
- {
- if (j != 0)
- {
- fprintf(fp, ", ");
- }
- fprintf(fp, "%d", vec[i][j]);
- }
- fprintf(fp, "}\n");
- }
- }
-}
-
-void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
- }
- }
-}
-
-void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
- }
- }
-}
-
-
-void pr_rvecs_len(FILE *fp, int indent, const char *title, const rvec vec[], int n)
-{
- int i, j;
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_nxn(fp, indent, title, n, DIM);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%5d]={", title, i);
- for (j = 0; j < DIM; j++)
- {
- if (j != 0)
- {
- fprintf(fp, ", ");
- }
- fprintf(fp, "%12.5e", vec[i][j]);
- }
- fprintf(fp, "} len=%12.5e\n", norm(vec[i]));
- }
- }
-}
-
-void pr_rvecs(FILE *fp, int indent, const char *title, const rvec vec[], int n)
-{
- const char *fshort = "%12.5e";
- const char *flong = "%15.8e";
- const char *format;
- int i, j;
-
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
- {
- format = flong;
- }
- else
- {
- format = fshort;
- }
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_nxn(fp, indent, title, n, DIM);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%5d]={", title, i);
- for (j = 0; j < DIM; j++)
- {
- if (j != 0)
- {
- fprintf(fp, ", ");
- }
- fprintf(fp, format, vec[i][j]);
- }
- fprintf(fp, "}\n");
- }
- }
-}
-
-
-void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim)
-{
- const char *fshort = "%12.5e";
- const char *flong = "%15.8e";
- const char *format;
- int i, j;
-
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
- {
- format = flong;
- }
- else
- {
- format = fshort;
- }
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_nxn(fp, indent, title, n, dim);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%5d]={", title, i);
- for (j = 0; j < dim; j++)
- {
- if (j != 0)
- {
- fprintf(fp, ", ");
- }
- fprintf(fp, format, vec[i][j]);
- }
- fprintf(fp, "}\n");
- }
- }
-}
-
-void pr_reals(FILE *fp, int indent, const char *title, const real *vec, int n)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s:\t", title);
- for (i = 0; i < n; i++)
- {
- fprintf(fp, " %10g", vec[i]);
- }
- fprintf(fp, "\n");
- }
-}
-
-void pr_doubles(FILE *fp, int indent, const char *title, const double *vec, int n)
-{
- int i;
-
- if (available(fp, vec, indent, title))
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s:\t", title);
- for (i = 0; i < n; i++)
- {
- fprintf(fp, " %10g", vec[i]);
- }
- fprintf(fp, "\n");
- }
-}
-
-void pr_reals_of_dim(FILE *fp, int indent, const char *title, const real *vec, int n, int dim)
-{
- int i, j;
- const char *fshort = "%12.5e";
- const char *flong = "%15.8e";
- const char *format;
-
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
- {
- format = flong;
- }
- else
- {
- format = fshort;
- }
-
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_nxn(fp, indent, title, n, dim);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%5d]={", title, i);
- for (j = 0; j < dim; j++)
- {
- if (j != 0)
- {
- fprintf(fp, ", ");
- }
- fprintf(fp, format, vec[i * dim + j]);
- }
- fprintf(fp, "}\n");
- }
- }
-}
-
-void pr_int(FILE *fp, int indent, const char *title, int i)
-{
- pr_indent(fp, indent);
- 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, "%-30s = %s\n", title, gmx_step_str(i, buf));
-}
-
-void pr_real(FILE *fp, int indent, const char *title, real r)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%-30s = %g\n", title, r);
-}
-
-void pr_double(FILE *fp, int indent, const char *title, double d)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%-30s = %g\n", title, d);
-}
-
-void pr_str(FILE *fp, int indent, const char *title, const char *s)
-{
- pr_indent(fp, indent);
- fprintf(fp, "%-30s = %s\n", title, s);
-}
-
-void pr_qm_opts(FILE *fp, int indent, const char *title, const t_grpopts *opts)
-{
- fprintf(fp, "%s:\n", title);
-
- pr_int(fp, indent, "ngQM", opts->ngQM);
- if (opts->ngQM > 0)
- {
- pr_ivec(fp, indent, "QMmethod", opts->QMmethod, opts->ngQM, FALSE);
- 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, "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, "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);
- }
-}
-
-static void pr_grp_opts(FILE *out, int indent, const char *title, const t_grpopts *opts,
- gmx_bool bMDPformat)
-{
- int i, m, j;
-
- if (!bMDPformat)
- {
- fprintf(out, "%s:\n", title);
- }
-
- pr_indent(out, indent);
- fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
- for (i = 0; (i < opts->ngtc); i++)
- {
- fprintf(out, " %10g", opts->nrdf[i]);
- }
- fprintf(out, "\n");
-
- pr_indent(out, indent);
- fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
- for (i = 0; (i < opts->ngtc); i++)
- {
- fprintf(out, " %10g", opts->ref_t[i]);
- }
- fprintf(out, "\n");
-
- pr_indent(out, indent);
- fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
- for (i = 0; (i < opts->ngtc); i++)
- {
- fprintf(out, " %10g", opts->tau_t[i]);
- }
- fprintf(out, "\n");
-
- /* Pretty-print the simulated annealing info */
- fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
- for (i = 0; (i < opts->ngtc); i++)
- {
- fprintf(out, " %10s", EANNEAL(opts->annealing[i]));
- }
- fprintf(out, "\n");
-
- fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":");
- for (i = 0; (i < opts->ngtc); i++)
- {
- fprintf(out, " %10d", opts->anneal_npoints[i]);
- }
- fprintf(out, "\n");
-
- for (i = 0; (i < opts->ngtc); i++)
- {
- if (opts->anneal_npoints[i] > 0)
- {
- 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, "annealing-temp [%d]:\t", i);
- for (j = 0; (j < opts->anneal_npoints[i]); j++)
- {
- fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
- }
- fprintf(out, "\n");
- }
- }
-
- pr_indent(out, indent);
- fprintf(out, "acc:\t");
- for (i = 0; (i < opts->ngacc); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- fprintf(out, " %10g", opts->acc[i][m]);
- }
- }
- fprintf(out, "\n");
-
- pr_indent(out, indent);
- fprintf(out, "nfreeze:");
- for (i = 0; (i < opts->ngfrz); i++)
- {
- for (m = 0; (m < DIM); m++)
- {
- fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
- }
- }
- fprintf(out, "\n");
-
-
- for (i = 0; (i < opts->ngener); i++)
- {
- pr_indent(out, indent);
- fprintf(out, "energygrp-flags[%3d]:", i);
- for (m = 0; (m < opts->ngener); m++)
- {
- fprintf(out, " %d", opts->egp_flags[opts->ngener*i+m]);
- }
- fprintf(out, "\n");
- }
-
- fflush(out);
-}
-
-static void pr_matrix(FILE *fp, int indent, const char *title, const rvec *m,
- gmx_bool bMDPformat)
-{
- if (bMDPformat)
- {
- fprintf(fp, "%-10s = %g %g %g %g %g %g\n", title,
- m[XX][XX], m[YY][YY], m[ZZ][ZZ], m[XX][YY], m[XX][ZZ], m[YY][ZZ]);
- }
- else
- {
- pr_rvecs(fp, indent, title, m, DIM);
- }
-}
-
-static void pr_cosine(FILE *fp, int indent, const char *title, const t_cosines *cos,
- gmx_bool bMDPformat)
-{
- int j;
-
- if (bMDPformat)
- {
- fprintf(fp, "%s = %d\n", title, cos->n);
- }
- else
- {
- indent = pr_title(fp, indent, title);
- pr_indent(fp, indent);
- fprintf(fp, "n = %d\n", cos->n);
- if (cos->n > 0)
- {
- pr_indent(fp, indent+2);
- fprintf(fp, "a =");
- for (j = 0; (j < cos->n); j++)
- {
- fprintf(fp, " %e", cos->a[j]);
- }
- fprintf(fp, "\n");
- pr_indent(fp, indent+2);
- fprintf(fp, "phi =");
- for (j = 0; (j < cos->n); j++)
- {
- fprintf(fp, " %e", cos->phi[j]);
- }
- fprintf(fp, "\n");
- }
- }
-}
-
-#define PS(t, s) pr_str(fp, indent, t, s)
-#define PI(t, s) pr_int(fp, indent, t, s)
-#define PSTEP(t, s) pr_int64(fp, indent, t, s)
-#define PR(t, s) pr_real(fp, indent, t, s)
-#define PD(t, s) pr_double(fp, indent, t, s)
-
-static void pr_pull_group(FILE *fp, int indent, int g, const t_pull_group *pgrp)
-{
- pr_indent(fp, indent);
- fprintf(fp, "pull-group %d:\n", g);
- indent += 2;
- pr_ivec_block(fp, indent, "atom", pgrp->ind, pgrp->nat, TRUE);
- pr_rvec(fp, indent, "weight", pgrp->weight, pgrp->nweight, TRUE);
- PI("pbcatom", pgrp->pbcatom);
-}
-
-static void pr_pull_coord(FILE *fp, int indent, int c, const t_pull_coord *pcrd)
-{
- int g;
-
- pr_indent(fp, indent);
- fprintf(fp, "pull-coord %d:\n", c);
- PS("type", EPULLTYPE(pcrd->eType));
- PS("geometry", EPULLGEOM(pcrd->eGeom));
- for (g = 0; g < pcrd->ngroup; g++)
- {
- char buf[10];
-
- sprintf(buf, "group[%d]", g);
- PI(buf, pcrd->group[g]);
- }
- pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
- pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
- pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
- PS("start", EBOOL(pcrd->bStart));
- PR("init", pcrd->init);
- PR("rate", pcrd->rate);
- PR("k", pcrd->k);
- PR("kB", pcrd->kB);
-}
-
-static void pr_simtempvals(FILE *fp, int indent, const t_simtemp *simtemp, int n_lambda)
-{
- 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);
-}
-
-static void pr_expandedvals(FILE *fp, int indent, const t_expanded *expand, int n_lambda)
-{
-
- PI("nstexpanded", expand->nstexpanded);
- 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)
- {
- PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
- }
- if (expand->elmceq == elmceqSAMPLES)
- {
- PI("weight-equil-number-samples", expand->equil_samples);
- }
- if (expand->elmceq == elmceqSTEPS)
- {
- PI("weight-equil-number-steps", expand->equil_steps);
- }
- if (expand->elmceq == elmceqWLDELTA)
- {
- PR("weight-equil-wl-delta", expand->equil_wl_delta);
- }
- if (expand->elmceq == elmceqRATIO)
- {
- 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);
- PS("init-weights", EBOOL(expand->bInit_weights));
-}
-
-static void pr_fepvals(FILE *fp, int indent, const t_lambda *fep, gmx_bool bMDPformat)
-{
- int i, j;
-
- 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);
- }
- if (fep->n_lambda > 0)
- {
- pr_indent(fp, indent);
- fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
- for (i = 0; i < efptNR; i++)
- {
- fprintf(fp, "%18s = ", efpt_names[i]);
- if (fep->separate_dvdl[i])
- {
- fprintf(fp, " TRUE");
- }
- else
- {
- fprintf(fp, " FALSE");
- }
- fprintf(fp, "\n");
- }
- fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
- for (i = 0; i < efptNR; i++)
- {
- fprintf(fp, "%18s = ", efpt_names[i]);
- for (j = 0; j < fep->n_lambda; j++)
- {
- fprintf(fp, " %10g", fep->all_lambda[i][j]);
- }
- fprintf(fp, "\n");
- }
- }
- PI("calc-lambda-neighbors", fep->lambda_neighbors);
- PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
- PR("sc-alpha", fep->sc_alpha);
- 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("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, const pull_params_t *pull)
-{
- int g;
-
- PR("pull-cylinder-r", pull->cylinder_r);
- PR("pull-constr-tol", pull->constr_tol);
- PS("pull-print-COM1", EBOOL(pull->bPrintCOM1));
- PS("pull-print-COM2", EBOOL(pull->bPrintCOM2));
- PS("pull-print-ref-value", EBOOL(pull->bPrintRefValue));
- PS("pull-print-components", EBOOL(pull->bPrintComp));
- PI("pull-nstxout", pull->nstxout);
- PI("pull-nstfout", pull->nstfout);
- PI("pull-ngroups", pull->ngroup);
- for (g = 0; g < pull->ngroup; g++)
- {
- pr_pull_group(fp, indent, g, &pull->group[g]);
- }
- 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, const t_rotgrp *rotg)
-{
- pr_indent(fp, indent);
- fprintf(fp, "rot-group %d:\n", g);
- indent += 2;
- 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, "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, const t_rot *rot)
-{
- int g;
-
- 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]);
- }
-}
-
-
-static void pr_swap(FILE *fp, int indent, const t_swapcoords *swap)
-{
- char str[STRLEN];
-
- /* Enums for better readability of the code */
- enum {
- eCompA = 0, eCompB
- };
-
-
- PI("swap-frequency", swap->nstswap);
-
- /* The split groups that define the compartments */
- for (int j = 0; j < 2; j++)
- {
- snprintf(str, STRLEN, "massw_split%d", j);
- PS(str, EBOOL(swap->massw_split[j]));
- snprintf(str, STRLEN, "split atoms group %d", j);
- pr_ivec_block(fp, indent, str, swap->grp[j].ind, swap->grp[j].nat, TRUE);
- }
-
- /* The solvent group */
- snprintf(str, STRLEN, "solvent group %s", swap->grp[eGrpSolvent].molname);
- pr_ivec_block(fp, indent, str, swap->grp[eGrpSolvent].ind, swap->grp[eGrpSolvent].nat, TRUE);
-
- /* Now print the indices for all the ion groups: */
- for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
- {
- snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
- pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
- }
-
- 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);
-
- /* Print the requested ion counts for both compartments */
- for (int ic = eCompA; ic <= eCompB; ic++)
- {
- for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
- {
- snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A'+ic);
- PI(str, swap->grp[ig].nmolReq[ic]);
- }
- }
-
- PR("threshold", swap->threshold);
- PR("bulk-offsetA", swap->bulkOffset[eCompA]);
- PR("bulk-offsetB", swap->bulkOffset[eCompB]);
-}
-
-
-static void pr_imd(FILE *fp, int indent, const t_IMD *imd)
-{
- PI("IMD-atoms", imd->nat);
- pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
-}
-
-
-void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
- gmx_bool bMDPformat)
-{
- const char *infbuf = "inf";
-
- if (available(fp, ir, indent, title))
- {
- if (!bMDPformat)
- {
- indent = pr_title(fp, indent, title);
- }
- /* 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);
- PI("simulation-part", ir->simulation_part);
- PS("comm-mode", ECOM(ir->comm_mode));
- 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("compressed-x-precision", ir->x_compression_precision);
-
- /* Neighborsearching parameters */
- PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme));
- PI("nstlist", ir->nstlist);
- PS("ns-type", ENS(ir->ns_type));
- PS("pbc", epbc_names[ir->ePBC]);
- PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
- PR("verlet-buffer-tolerance", ir->verletbuf_tol);
- PR("rlist", ir->rlist);
-
- /* 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);
- if (ir->epsilon_r != 0)
- {
- PR("epsilon-r", ir->epsilon_r);
- }
- else
- {
- PS("epsilon-r", infbuf);
- }
- if (ir->epsilon_rf != 0)
- {
- PR("epsilon-rf", ir->epsilon_rf);
- }
- else
- {
- PS("epsilon-rf", infbuf);
- }
- 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));
- 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-obc-gamma", ir->gb_obc_gamma);
- PR("gb-dielectric-offset", ir->gb_dielectric_offset);
- PS("sa-algorithm", ESAALGORITHM(ir->sa_algorithm));
- PR("sa-surface-tension", ir->sa_surface_tension);
-
- /* 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)
- {
- 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]);
- }
- else
- {
- 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", EBOOL(ir->bPull));
- if (ir->bPull)
- {
- 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("orire-fc", ir->orires_fc);
- PR("orire-tau", ir->orires_tau);
- PR("nstorireout", ir->nstorireout);
-
- /* 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);
- }
-
- /* 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);
- }
-
- /* USER-DEFINED THINGIES */
- PI("userint1", ir->userint1);
- PI("userint2", ir->userint2);
- PI("userint3", ir->userint3);
- PI("userint4", ir->userint4);
- PR("userreal1", ir->userreal1);
- PR("userreal2", ir->userreal2);
- PR("userreal3", ir->userreal3);
- PR("userreal4", ir->userreal4);
-
- pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
- }
-}
-#undef PS
-#undef PR
-#undef PI
-
-void pr_strings(FILE *fp, int indent, const char *title, char ***nm, int n, gmx_bool bShowNumbers)
-{
- int i;
-
- if (available(fp, nm, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]={name=\"%s\"}\n",
- title, bShowNumbers ? i : -1, *(nm[i]));
- }
- }
-}
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
{
d[m] = std::sqrt(d[m]/tm);
}
-#ifdef DEBUG
- pr_rvecs(stderr, 0, "trans", trans, DIM);
-#endif
/* rotate_atoms(gnx,index,x,trans); */
}
clear_rvec(comp);
#include <climits>
#include <cmath>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/ifunc.h"
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/topdirs.h"
#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gmxpre.h"
#include "gromacs/fileio/trrio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/copyrite.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/readinp.h"
#include "gromacs/gmxpreprocess/gen_ad.h"
#include "gromacs/gmxpreprocess/gpp_nextnb.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/symtab.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "vecdump.h"
+
+#include <cstdio>
+#include <cstdlib>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/txtdump.h"
+
+void pr_ivec(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%d\n", title, bShowNumbers ? i : -1, vec[i]);
+ }
+ }
+}
+
+void pr_ivec_block(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers)
+{
+ int i, j;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ i = 0;
+ while (i < n)
+ {
+ j = i+1;
+ while (j < n && vec[j] == vec[j-1]+1)
+ {
+ j++;
+ }
+ /* Print consecutive groups of 3 or more as blocks */
+ if (j - i < 3)
+ {
+ while (i < j)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%d\n",
+ title, bShowNumbers ? i : -1, vec[i]);
+ i++;
+ }
+ }
+ else
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d,...,%d] = {%d,...,%d}\n",
+ title,
+ bShowNumbers ? i : -1,
+ bShowNumbers ? j-1 : -1,
+ vec[i], vec[j-1]);
+ i = j;
+ }
+ }
+ }
+}
+
+void pr_bvec(FILE *fp, int indent, const char *title, const gmx_bool vec[], int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%s\n", title, bShowNumbers ? i : -1,
+ gmx::boolToString(vec[i]));
+ }
+ }
+}
+
+void pr_ivecs(FILE *fp, int indent, const char *title, const ivec vec[], int n, gmx_bool bShowNumbers)
+{
+ int i, j;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, DIM);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]={", title, bShowNumbers ? i : -1);
+ for (j = 0; j < DIM; j++)
+ {
+ if (j != 0)
+ {
+ fprintf(fp, ", ");
+ }
+ fprintf(fp, "%d", vec[i][j]);
+ }
+ fprintf(fp, "}\n");
+ }
+ }
+}
+
+void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
+ }
+ }
+}
+
+void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
+ }
+ }
+}
+
+
+void pr_rvecs_len(FILE *fp, int indent, const char *title, const rvec vec[], int n)
+{
+ int i, j;
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, DIM);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < DIM; j++)
+ {
+ if (j != 0)
+ {
+ fprintf(fp, ", ");
+ }
+ fprintf(fp, "%12.5e", vec[i][j]);
+ }
+ fprintf(fp, "} len=%12.5e\n", norm(vec[i]));
+ }
+ }
+}
+
+void pr_rvecs(FILE *fp, int indent, const char *title, const rvec vec[], int n)
+{
+ const char *fshort = "%12.5e";
+ const char *flong = "%15.8e";
+ const char *format;
+ int i, j;
+
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ {
+ format = flong;
+ }
+ else
+ {
+ format = fshort;
+ }
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, DIM);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < DIM; j++)
+ {
+ if (j != 0)
+ {
+ fprintf(fp, ", ");
+ }
+ fprintf(fp, format, vec[i][j]);
+ }
+ fprintf(fp, "}\n");
+ }
+ }
+}
+
+
+void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim)
+{
+ const char *fshort = "%12.5e";
+ const char *flong = "%15.8e";
+ const char *format;
+ int i, j;
+
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ {
+ format = flong;
+ }
+ else
+ {
+ format = fshort;
+ }
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, dim);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < dim; j++)
+ {
+ if (j != 0)
+ {
+ fprintf(fp, ", ");
+ }
+ fprintf(fp, format, vec[i][j]);
+ }
+ fprintf(fp, "}\n");
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MATH_VECDUMP_H
+#define GMX_MATH_VECDUMP_H
+
+#include <cstdio>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
+void pr_ivec(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers);
+void pr_ivec_block(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers);
+void pr_ivecs(FILE *fp, int indent, const char *title, const ivec vec[], int n, gmx_bool bShowNumbers);
+void pr_bvec(FILE *fp, int indent, const char *title, const gmx_bool vec[], int n, gmx_bool bShowNnumbers);
+void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers);
+void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim);
+void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers);
+void pr_rvecs(FILE *fp, int indent, const char *title, const rvec vec[], int n);
+void pr_rvecs_len(FILE *fp, int indent, const char *title, const rvec vec[], int n);
+
+#endif
#include "gromacs/fileio/copyrite.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/splitter.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
typedef struct gmx_constr {
int ncon_tot; /* The total number of constraints */
#include <algorithm>
#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/ewald/ewald.h"
#include "gromacs/ewald/long-range-correction.h"
#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/listed-forces/listed-forces.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/forcerec-threading.h"
#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/nsgrid.h"
#include "gromacs/mdlib/qmmm.h"
ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
}
-#ifdef DEBUG
- pr_nsblock(log);
-#endif
-
inc_nrnb(nrnb, eNR_NS, nsearch);
return nsearch;
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/copyrite.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/gmxlib/disre.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/calcmu.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/disre.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/orires.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/mdrun.h"
#include "vcm.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
#include "inputrec.h"
+#include <cstdio>
#include <cstring>
#include <algorithm>
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/txtdump.h"
+
+//! Macro to select a bool name
+#define EBOOL(e) gmx::boolToString(e)
/* The minimum number of integration steps required for reasonably accurate
* integration of first and second order coupling algorithms.
}
}
+static void pr_qm_opts(FILE *fp, int indent, const char *title, const t_grpopts *opts)
+{
+ fprintf(fp, "%s:\n", title);
+
+ pr_int(fp, indent, "ngQM", opts->ngQM);
+ if (opts->ngQM > 0)
+ {
+ pr_ivec(fp, indent, "QMmethod", opts->QMmethod, opts->ngQM, FALSE);
+ 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, "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, "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);
+ }
+}
+
+static void pr_grp_opts(FILE *out, int indent, const char *title, const t_grpopts *opts,
+ gmx_bool bMDPformat)
+{
+ int i, m, j;
+
+ if (!bMDPformat)
+ {
+ fprintf(out, "%s:\n", title);
+ }
+
+ pr_indent(out, indent);
+ fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ fprintf(out, " %10g", opts->nrdf[i]);
+ }
+ fprintf(out, "\n");
+
+ pr_indent(out, indent);
+ fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ fprintf(out, " %10g", opts->ref_t[i]);
+ }
+ fprintf(out, "\n");
+
+ pr_indent(out, indent);
+ fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ fprintf(out, " %10g", opts->tau_t[i]);
+ }
+ fprintf(out, "\n");
+
+ /* Pretty-print the simulated annealing info */
+ fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ fprintf(out, " %10s", EANNEAL(opts->annealing[i]));
+ }
+ fprintf(out, "\n");
+
+ fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":");
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ fprintf(out, " %10d", opts->anneal_npoints[i]);
+ }
+ fprintf(out, "\n");
+
+ for (i = 0; (i < opts->ngtc); i++)
+ {
+ if (opts->anneal_npoints[i] > 0)
+ {
+ 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, "annealing-temp [%d]:\t", i);
+ for (j = 0; (j < opts->anneal_npoints[i]); j++)
+ {
+ fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
+ }
+ fprintf(out, "\n");
+ }
+ }
+
+ pr_indent(out, indent);
+ fprintf(out, "acc:\t");
+ for (i = 0; (i < opts->ngacc); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ fprintf(out, " %10g", opts->acc[i][m]);
+ }
+ }
+ fprintf(out, "\n");
+
+ pr_indent(out, indent);
+ fprintf(out, "nfreeze:");
+ for (i = 0; (i < opts->ngfrz); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
+ }
+ }
+ fprintf(out, "\n");
+
+
+ for (i = 0; (i < opts->ngener); i++)
+ {
+ pr_indent(out, indent);
+ fprintf(out, "energygrp-flags[%3d]:", i);
+ for (m = 0; (m < opts->ngener); m++)
+ {
+ fprintf(out, " %d", opts->egp_flags[opts->ngener*i+m]);
+ }
+ fprintf(out, "\n");
+ }
+
+ fflush(out);
+}
+
+static void pr_matrix(FILE *fp, int indent, const char *title, const rvec *m,
+ gmx_bool bMDPformat)
+{
+ if (bMDPformat)
+ {
+ fprintf(fp, "%-10s = %g %g %g %g %g %g\n", title,
+ m[XX][XX], m[YY][YY], m[ZZ][ZZ], m[XX][YY], m[XX][ZZ], m[YY][ZZ]);
+ }
+ else
+ {
+ pr_rvecs(fp, indent, title, m, DIM);
+ }
+}
+
+static void pr_cosine(FILE *fp, int indent, const char *title, const t_cosines *cos,
+ gmx_bool bMDPformat)
+{
+ int j;
+
+ if (bMDPformat)
+ {
+ fprintf(fp, "%s = %d\n", title, cos->n);
+ }
+ else
+ {
+ indent = pr_title(fp, indent, title);
+ pr_indent(fp, indent);
+ fprintf(fp, "n = %d\n", cos->n);
+ if (cos->n > 0)
+ {
+ pr_indent(fp, indent+2);
+ fprintf(fp, "a =");
+ for (j = 0; (j < cos->n); j++)
+ {
+ fprintf(fp, " %e", cos->a[j]);
+ }
+ fprintf(fp, "\n");
+ pr_indent(fp, indent+2);
+ fprintf(fp, "phi =");
+ for (j = 0; (j < cos->n); j++)
+ {
+ fprintf(fp, " %e", cos->phi[j]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+}
+
+#define PS(t, s) pr_str(fp, indent, t, s)
+#define PI(t, s) pr_int(fp, indent, t, s)
+#define PSTEP(t, s) pr_int64(fp, indent, t, s)
+#define PR(t, s) pr_real(fp, indent, t, s)
+#define PD(t, s) pr_double(fp, indent, t, s)
+
+static void pr_pull_group(FILE *fp, int indent, int g, const t_pull_group *pgrp)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "pull-group %d:\n", g);
+ indent += 2;
+ pr_ivec_block(fp, indent, "atom", pgrp->ind, pgrp->nat, TRUE);
+ pr_rvec(fp, indent, "weight", pgrp->weight, pgrp->nweight, TRUE);
+ PI("pbcatom", pgrp->pbcatom);
+}
+
+static void pr_pull_coord(FILE *fp, int indent, int c, const t_pull_coord *pcrd)
+{
+ int g;
+
+ pr_indent(fp, indent);
+ fprintf(fp, "pull-coord %d:\n", c);
+ PS("type", EPULLTYPE(pcrd->eType));
+ PS("geometry", EPULLGEOM(pcrd->eGeom));
+ for (g = 0; g < pcrd->ngroup; g++)
+ {
+ char buf[10];
+
+ sprintf(buf, "group[%d]", g);
+ PI(buf, pcrd->group[g]);
+ }
+ pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
+ pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
+ pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
+ PS("start", EBOOL(pcrd->bStart));
+ PR("init", pcrd->init);
+ PR("rate", pcrd->rate);
+ PR("k", pcrd->k);
+ PR("kB", pcrd->kB);
+}
+
+static void pr_simtempvals(FILE *fp, int indent, const t_simtemp *simtemp, int n_lambda)
+{
+ 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);
+}
+
+static void pr_expandedvals(FILE *fp, int indent, const t_expanded *expand, int n_lambda)
+{
+
+ PI("nstexpanded", expand->nstexpanded);
+ 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)
+ {
+ PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
+ }
+ if (expand->elmceq == elmceqSAMPLES)
+ {
+ PI("weight-equil-number-samples", expand->equil_samples);
+ }
+ if (expand->elmceq == elmceqSTEPS)
+ {
+ PI("weight-equil-number-steps", expand->equil_steps);
+ }
+ if (expand->elmceq == elmceqWLDELTA)
+ {
+ PR("weight-equil-wl-delta", expand->equil_wl_delta);
+ }
+ if (expand->elmceq == elmceqRATIO)
+ {
+ 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);
+ PS("init-weights", EBOOL(expand->bInit_weights));
+}
+
+static void pr_fepvals(FILE *fp, int indent, const t_lambda *fep, gmx_bool bMDPformat)
+{
+ int i, j;
+
+ 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);
+ }
+ if (fep->n_lambda > 0)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
+ for (i = 0; i < efptNR; i++)
+ {
+ fprintf(fp, "%18s = ", efpt_names[i]);
+ if (fep->separate_dvdl[i])
+ {
+ fprintf(fp, " TRUE");
+ }
+ else
+ {
+ fprintf(fp, " FALSE");
+ }
+ fprintf(fp, "\n");
+ }
+ fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
+ for (i = 0; i < efptNR; i++)
+ {
+ fprintf(fp, "%18s = ", efpt_names[i]);
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ fprintf(fp, " %10g", fep->all_lambda[i][j]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+ PI("calc-lambda-neighbors", fep->lambda_neighbors);
+ PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
+ PR("sc-alpha", fep->sc_alpha);
+ 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("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, const pull_params_t *pull)
+{
+ int g;
+
+ PR("pull-cylinder-r", pull->cylinder_r);
+ PR("pull-constr-tol", pull->constr_tol);
+ PS("pull-print-COM1", EBOOL(pull->bPrintCOM1));
+ PS("pull-print-COM2", EBOOL(pull->bPrintCOM2));
+ PS("pull-print-ref-value", EBOOL(pull->bPrintRefValue));
+ PS("pull-print-components", EBOOL(pull->bPrintComp));
+ PI("pull-nstxout", pull->nstxout);
+ PI("pull-nstfout", pull->nstfout);
+ PI("pull-ngroups", pull->ngroup);
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ pr_pull_group(fp, indent, g, &pull->group[g]);
+ }
+ 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, const t_rotgrp *rotg)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "rot-group %d:\n", g);
+ indent += 2;
+ 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, "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, const t_rot *rot)
+{
+ int g;
+
+ 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]);
+ }
+}
+
+
+static void pr_swap(FILE *fp, int indent, const t_swapcoords *swap)
+{
+ char str[STRLEN];
+
+ /* Enums for better readability of the code */
+ enum {
+ eCompA = 0, eCompB
+ };
+
+
+ PI("swap-frequency", swap->nstswap);
+
+ /* The split groups that define the compartments */
+ for (int j = 0; j < 2; j++)
+ {
+ snprintf(str, STRLEN, "massw_split%d", j);
+ PS(str, EBOOL(swap->massw_split[j]));
+ snprintf(str, STRLEN, "split atoms group %d", j);
+ pr_ivec_block(fp, indent, str, swap->grp[j].ind, swap->grp[j].nat, TRUE);
+ }
+
+ /* The solvent group */
+ snprintf(str, STRLEN, "solvent group %s", swap->grp[eGrpSolvent].molname);
+ pr_ivec_block(fp, indent, str, swap->grp[eGrpSolvent].ind, swap->grp[eGrpSolvent].nat, TRUE);
+
+ /* Now print the indices for all the ion groups: */
+ for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
+ {
+ snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
+ pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
+ }
+
+ 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);
+
+ /* Print the requested ion counts for both compartments */
+ for (int ic = eCompA; ic <= eCompB; ic++)
+ {
+ for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
+ {
+ snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A'+ic);
+ PI(str, swap->grp[ig].nmolReq[ic]);
+ }
+ }
+
+ PR("threshold", swap->threshold);
+ PR("bulk-offsetA", swap->bulkOffset[eCompA]);
+ PR("bulk-offsetB", swap->bulkOffset[eCompB]);
+}
+
+
+static void pr_imd(FILE *fp, int indent, const t_IMD *imd)
+{
+ PI("IMD-atoms", imd->nat);
+ pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
+}
+
+
+void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
+ gmx_bool bMDPformat)
+{
+ const char *infbuf = "inf";
+
+ if (available(fp, ir, indent, title))
+ {
+ if (!bMDPformat)
+ {
+ indent = pr_title(fp, indent, title);
+ }
+ /* 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);
+ PI("simulation-part", ir->simulation_part);
+ PS("comm-mode", ECOM(ir->comm_mode));
+ 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("compressed-x-precision", ir->x_compression_precision);
+
+ /* Neighborsearching parameters */
+ PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme));
+ PI("nstlist", ir->nstlist);
+ PS("ns-type", ENS(ir->ns_type));
+ PS("pbc", epbc_names[ir->ePBC]);
+ PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
+ PR("verlet-buffer-tolerance", ir->verletbuf_tol);
+ PR("rlist", ir->rlist);
+
+ /* 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);
+ if (ir->epsilon_r != 0)
+ {
+ PR("epsilon-r", ir->epsilon_r);
+ }
+ else
+ {
+ PS("epsilon-r", infbuf);
+ }
+ if (ir->epsilon_rf != 0)
+ {
+ PR("epsilon-rf", ir->epsilon_rf);
+ }
+ else
+ {
+ PS("epsilon-rf", infbuf);
+ }
+ 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));
+ 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-obc-gamma", ir->gb_obc_gamma);
+ PR("gb-dielectric-offset", ir->gb_dielectric_offset);
+ PS("sa-algorithm", ESAALGORITHM(ir->sa_algorithm));
+ PR("sa-surface-tension", ir->sa_surface_tension);
+
+ /* 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)
+ {
+ 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]);
+ }
+ else
+ {
+ 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", EBOOL(ir->bPull));
+ if (ir->bPull)
+ {
+ 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("orire-fc", ir->orires_fc);
+ PR("orire-tau", ir->orires_tau);
+ PR("nstorireout", ir->nstorireout);
+
+ /* 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);
+ }
+
+ /* 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);
+ }
+
+ /* USER-DEFINED THINGIES */
+ PI("userint1", ir->userint1);
+ PI("userint2", ir->userint2);
+ PI("userint3", ir->userint3);
+ PI("userint4", ir->userint4);
+ PR("userreal1", ir->userreal1);
+ PR("userreal2", ir->userreal2);
+ PR("userreal3", ir->userreal3);
+ PR("userreal4", ir->userreal4);
+
+ pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
+ }
+}
+#undef PS
+#undef PR
+#undef PI
+
gmx_bool inputrecDeform(const t_inputrec *ir)
{
return (ir->deform[XX][XX] != 0 || ir->deform[YY][YY] != 0 || ir->deform[ZZ][ZZ] != 0 ||
#ifndef GMX_MDTYPES_INPUTREC_H
#define GMX_MDTYPES_INPUTREC_H
+#include <stdio.h>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
*/
void done_inputrec(t_inputrec *ir);
+void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
+ gmx_bool bMDPformat);
+
gmx_bool inputrecDeform(const t_inputrec *ir);
gmx_bool inputrecDynamicBox(const t_inputrec *ir);
#include <algorithm>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxpreprocess/gmxcpp.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
gmx_bool bSysTop)
#include <cstdio>
#include <cstring>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
const char *ptype_str[eptNR+1] = {
"Atom", "Nucleus", "Shell", "Bond", "VSite", NULL
#include <algorithm>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
void init_block(t_block *block)
{
#include <cstdio>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/ifunc.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/txtdump.h"
static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
{
#include <algorithm>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
#define BUFSIZE 1024
#define TABLESIZE 5
#include <algorithm>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/ifunc.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/txtdump.h"
const char *gtypes[egcNR+1] = {
"T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+/* This file is completely threadsafe - please keep it that way! */
+
+#include "txtdump.h"
+
+#include <cstdio>
+#include <cstdlib>
+
+#include "gromacs/utility/cstringutil.h"
+
+int pr_indent(FILE *fp, int n)
+{
+ int i;
+
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fp, " ");
+ }
+ return n;
+}
+
+int available(FILE *fp, const void *p, int indent, const char *title)
+{
+ if (!p)
+ {
+ if (indent > 0)
+ {
+ pr_indent(fp, indent);
+ }
+ fprintf(fp, "%s: not available\n", title);
+ }
+ return (p != NULL);
+}
+
+int pr_title(FILE *fp, int indent, const char *title)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%s:\n", title);
+ return (indent+INDENT);
+}
+
+int pr_title_n(FILE *fp, int indent, const char *title, int n)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%s (%d):\n", title, n);
+ return (indent+INDENT);
+}
+
+int pr_title_nxn(FILE *fp, int indent, const char *title, int n1, int n2)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%s (%dx%d):\n", title, n1, n2);
+ return (indent+INDENT);
+}
+
+void pr_reals(FILE *fp, int indent, const char *title, const real *vec, int n)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s:\t", title);
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fp, " %10g", vec[i]);
+ }
+ fprintf(fp, "\n");
+ }
+}
+
+void pr_doubles(FILE *fp, int indent, const char *title, const double *vec, int n)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s:\t", title);
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fp, " %10g", vec[i]);
+ }
+ fprintf(fp, "\n");
+ }
+}
+
+void pr_reals_of_dim(FILE *fp, int indent, const char *title, const real *vec, int n, int dim)
+{
+ int i, j;
+ const char *fshort = "%12.5e";
+ const char *flong = "%15.8e";
+ const char *format;
+
+ if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ {
+ format = flong;
+ }
+ else
+ {
+ format = fshort;
+ }
+
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, dim);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < dim; j++)
+ {
+ if (j != 0)
+ {
+ fprintf(fp, ", ");
+ }
+ fprintf(fp, format, vec[i * dim + j]);
+ }
+ fprintf(fp, "}\n");
+ }
+ }
+}
+
+void pr_int(FILE *fp, int indent, const char *title, int i)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %d\n", title, i);
+}
+
+void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i)
+{
+ char buf[STEPSTRSIZE];
+
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %s\n", title, gmx_step_str(i, buf));
+}
+
+void pr_real(FILE *fp, int indent, const char *title, real r)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %g\n", title, r);
+}
+
+void pr_double(FILE *fp, int indent, const char *title, double d)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %g\n", title, d);
+}
+
+void pr_str(FILE *fp, int indent, const char *title, const char *s)
+{
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %s\n", title, s);
+}
+
+void pr_strings(FILE *fp, int indent, const char *title, char ***nm, int n, gmx_bool bShowNumbers)
+{
+ int i;
+
+ if (available(fp, nm, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]={name=\"%s\"}\n",
+ title, bShowNumbers ? i : -1, *(nm[i]));
+ }
+ }
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief
+ * Declares helper functions for dumping basic data structures as text.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
#ifndef GMX_FILEIO_TXTDUMP_H
#define GMX_FILEIO_TXTDUMP_H
#include <cstdio>
-#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
-struct t_inputrec;
-
+//! Line width for text dump output.
#define LINE_WIDTH 80
+//! Right margin for text dump output.
#define RMARGIN 10
+//! Actual line length for text dump output.
#define USE_WIDTH ((LINE_WIDTH)-(RMARGIN))
+//! Default indentation for text dump output.
#define INDENT 3
+//! Prints an initial indentation for a line.
int pr_indent(FILE *fp, int n);
+//! Returns whether \p is available (not null), and prints a note if it is not.
int available(FILE *fp, const void *p, int indent, const char *title);
+//! Prints a title for a dumped section.
int pr_title(FILE *fp, int indent, const char *title);
+//! Prints a title for a dumped section with a number suffixed.
int pr_title_n(FILE *fp, int indent, const char *title, int n);
+//! Prints a title for a dumped section with two numbers suffixed (in NxM format).
int pr_title_nxn(FILE *fp, int indent, const char *title, int n1, int n2);
-void pr_ivec(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers);
-void pr_ivecs(FILE *fp, int indent, const char *title, const ivec vec[], int n, gmx_bool bShowNumbers);
-void pr_bvec(FILE *fp, int indent, const char *title, const gmx_bool vec[], int n, gmx_bool bShowNnumbers);
-void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers);
-void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim);
-void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers);
-void pr_rvecs(FILE *fp, int indent, const char *title, const rvec vec[], int n);
-void pr_rvecs_len(FILE *fp, int indent, const char *title, const rvec vec[], int n);
+//! Prints an array of reals.
void pr_reals(FILE *fp, int indent, const char *title, const real vec[], int n);
+//! Prints an array of doubles.
void pr_doubles(FILE *fp, int indent, const char *title, const double *vec, int n);
+//! Prints an array of reals as a matrix with inner dimension dim.
void pr_reals_of_dim(FILE *fp, int indent, const char *title, const real *vec, int n, int dim);
+//! Prints an integer value.
void pr_int(FILE *fp, int indent, const char *title, int i);
+//! Prints a gmx_int64_t value.
+void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i);
+//! Prints a floating-point value.
void pr_real(FILE *fp, int indent, const char *title, real r);
+//! Prints a double-precision floating-point value.
void pr_double(FILE *fp, int indent, const char *title, double d);
+//! Prints a string value.
void pr_str(FILE *fp, int indent, const char *title, const char *s);
+//! Prints strings as a section; intended to be used for an array of names.
void pr_strings(FILE *fp, int indent, const char *title, char ***nm, int n, gmx_bool bShowNumbers);
-void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
- gmx_bool bMDPformat);
#endif
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/disre.h"
#include "gromacs/gmxlib/gmx_detect_hardware.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include <cstdlib>
#include <cstring>
-#include "gromacs/fileio/txtdump.h"
#include "gromacs/math/vec.h"
+#include "gromacs/math/vecdump.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff