-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * 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! */
-#ifdef GMX_THREAD_MPI
-#include <thread_mpi.h>
-#endif
+#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)
+int pr_indent(FILE *fp, int n)
{
- int i;
+ int i;
- for (i=0; i<n; i++) (void) fprintf(fp," ");
- return n;
+ for (i = 0; i < n; i++)
+ {
+ (void) fprintf(fp, " ");
+ }
+ return n;
}
-int available(FILE *fp,void *p,int indent,const char *title)
+int available(FILE *fp, void *p, int indent, const char *title)
{
- if (!p) {
- if (indent > 0)
- pr_indent(fp,indent);
- (void) fprintf(fp,"%s: not available\n",title);
- }
- return (p!=NULL);
+ if (!p)
+ {
+ if (indent > 0)
+ {
+ pr_indent(fp, indent);
+ }
+ (void) fprintf(fp, "%s: not available\n", title);
+ }
+ return (p != NULL);
}
-int pr_title(FILE *fp,int indent,const char *title)
+int pr_title(FILE *fp, int indent, const char *title)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s:\n",title);
- return (indent+INDENT);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s:\n", title);
+ return (indent+INDENT);
}
-int pr_title_n(FILE *fp,int indent,const char *title,int n)
+int pr_title_n(FILE *fp, int indent, const char *title, int n)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s (%d):\n",title,n);
- return (indent+INDENT);
+ (void) pr_indent(fp, indent);
+ (void) 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)
+int pr_title_nxn(FILE *fp, int indent, const char *title, int n1, int n2)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s (%dx%d):\n",title,n1,n2);
- return (indent+INDENT);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s (%dx%d):\n", title, n1, n2);
+ return (indent+INDENT);
}
-void pr_ivec(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
+void pr_ivec(FILE *fp, int indent, const char *title, int vec[], int n, gmx_bool bShowNumbers)
{
- int i;
+ int i;
- if (available(fp,vec,indent,title))
+ if (available(fp, vec, indent, title))
{
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++)
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]=%d\n",title,bShowNumbers?i:-1,vec[i]);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]=%d\n", title, bShowNumbers ? i : -1, vec[i]);
}
}
}
-void pr_ivec_block(FILE *fp,int indent,const char *title,int vec[],int n, gmx_bool bShowNumbers)
+void pr_ivec_block(FILE *fp, int indent, const char *title, int vec[], int n, gmx_bool bShowNumbers)
{
- int i,j;
-
- if (available(fp,vec,indent,title))
+ int i, j;
+
+ if (available(fp, vec, indent, title))
{
- indent=pr_title_n(fp,indent,title,n);
- i = 0;
+ indent = pr_title_n(fp, indent, title, n);
+ i = 0;
while (i < n)
{
j = i+1;
/* Print consecutive groups of 3 or more as blocks */
if (j - i < 3)
{
- while(i < j)
+ while (i < j)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]=%d\n",
- title,bShowNumbers?i:-1,vec[i]);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]=%d\n",
+ title, bShowNumbers ? i : -1, vec[i]);
i++;
}
}
else
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d,...,%d] = {%d,...,%d}\n",
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d,...,%d] = {%d,...,%d}\n",
title,
- bShowNumbers?i:-1,
- bShowNumbers?j-1:-1,
- vec[i],vec[j-1]);
+ bShowNumbers ? i : -1,
+ bShowNumbers ? j-1 : -1,
+ vec[i], vec[j-1]);
i = j;
}
}
}
}
-void pr_bvec(FILE *fp,int indent,const char *title,gmx_bool vec[],int n, gmx_bool bShowNumbers)
+void pr_bvec(FILE *fp, int indent, const char *title, gmx_bool vec[], int n, gmx_bool bShowNumbers)
{
- int i;
+ int i;
- if (available(fp,vec,indent,title))
+ if (available(fp, vec, indent, title))
{
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++)
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]=%s\n",title,bShowNumbers?i:-1,
- EBOOL(vec[i]));
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]=%s\n", title, bShowNumbers ? i : -1,
+ EBOOL(vec[i]));
}
}
}
-void pr_ivecs(FILE *fp,int indent,const char *title,ivec vec[],int n, gmx_bool bShowNumbers)
+void pr_ivecs(FILE *fp, int indent, const char *title, ivec vec[], int n, gmx_bool bShowNumbers)
{
- int i,j;
+ int i, j;
- if (available(fp,vec,indent,title))
- {
- indent=pr_title_nxn(fp,indent,title,n,DIM);
- for (i=0; i<n; i++)
+ if (available(fp, vec, indent, title))
+ {
+ indent = pr_title_nxn(fp, indent, title, n, DIM);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]={",title,bShowNumbers?i:-1);
- for (j=0; j<DIM; j++)
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]={", title, bShowNumbers ? i : -1);
+ for (j = 0; j < DIM; j++)
{
- if (j!=0) (void) fprintf(fp,", ");
- fprintf(fp,"%d",vec[i][j]);
+ if (j != 0)
+ {
+ (void) fprintf(fp, ", ");
+ }
+ fprintf(fp, "%d", vec[i][j]);
}
- (void) fprintf(fp,"}\n");
+ (void) fprintf(fp, "}\n");
}
}
}
-void pr_rvec(FILE *fp,int indent,const char *title,real vec[],int n, gmx_bool bShowNumbers)
+void pr_rvec(FILE *fp, int indent, const char *title, real vec[], int n, gmx_bool bShowNumbers)
{
- int i;
+ int i;
- if (available(fp,vec,indent,title))
- {
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; 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]);
+ 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,double vec[],int n, gmx_bool bShowNumbers)
+void pr_dvec(FILE *fp, int indent, const char *title, 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++)
+ 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]);
+ pr_indent(fp, indent);
+ fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
}
}
}
/*
-void pr_mat(FILE *fp,int indent,char *title,matrix m)
-{
- int i,j;
-
- if (available(fp,m,indent,title)) {
+ void pr_mat(FILE *fp,int indent,char *title,matrix m)
+ {
+ int i,j;
+
+ if (available(fp,m,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 %12.5e %12.5e\n",
- title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
+ title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
+ }
+ }
+ }
+ */
+
+void pr_rvecs_len(FILE *fp, int indent, const char *title, 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++)
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < DIM; j++)
+ {
+ if (j != 0)
+ {
+ (void) fprintf(fp, ", ");
+ }
+ (void) fprintf(fp, "%12.5e", vec[i][j]);
+ }
+ (void) fprintf(fp, "} len=%12.5e\n", norm(vec[i]));
+ }
}
- }
}
-*/
-void pr_rvecs_len(FILE *fp,int indent,const char *title,rvec vec[],int n)
+void pr_rvecs(FILE *fp, int indent, const char *title, 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++) {
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%5d]={",title,i);
- for (j=0; j<DIM; j++) {
- if (j != 0)
- (void) fprintf(fp,", ");
- (void) fprintf(fp,"%12.5e",vec[i][j]);
- }
- (void) fprintf(fp,"} len=%12.5e\n",norm(vec[i]));
- }
- }
+ 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++)
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < DIM; j++)
+ {
+ if (j != 0)
+ {
+ (void) fprintf(fp, ", ");
+ }
+ (void) fprintf(fp, format, vec[i][j]);
+ }
+ (void) fprintf(fp, "}\n");
+ }
+ }
}
-void pr_rvecs(FILE *fp,int indent,const char *title,rvec vec[],int n)
+
+void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, rvec vec[], int n, int dim)
{
- const char *fshort = "%12.5e";
- const char *flong = "%15.8e";
- const char *format;
- int i,j;
-
- if (getenv("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++) {
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%5d]={",title,i);
- for (j=0; j<DIM; j++) {
- if (j != 0)
- (void) fprintf(fp,", ");
- (void) fprintf(fp,format,vec[i][j]);
- }
- (void) fprintf(fp,"}\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++)
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < dim; j++)
+ {
+ if (j != 0)
+ {
+ (void) fprintf(fp, ", ");
+ }
+ (void) fprintf(fp, format, vec[i][j]);
+ }
+ (void) fprintf(fp, "}\n");
+ }
+ }
}
+void pr_reals(FILE *fp, int indent, const char *title, real *vec, int n)
+{
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s:\t", title);
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fp, " %10g", vec[i]);
+ }
+ (void) fprintf(fp, "\n");
+ }
+}
-void pr_reals(FILE *fp,int indent,const char *title,real *vec,int n)
+void pr_doubles(FILE *fp, int indent, const char *title, double *vec, int n)
{
- int i;
-
- if (available(fp,vec,indent,title)) {
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s:\t",title);
- for(i=0; i<n; i++)
- fprintf(fp," %10g",vec[i]);
- (void) fprintf(fp,"\n");
- }
+ int i;
+
+ if (available(fp, vec, indent, title))
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s:\t", title);
+ for (i = 0; i < n; i++)
+ {
+ fprintf(fp, " %10g", vec[i]);
+ }
+ (void) fprintf(fp, "\n");
+ }
}
-void pr_doubles(FILE *fp,int indent,const char *title,double *vec,int n)
+void pr_reals_of_dim(FILE *fp, int indent, const char *title, real *vec, int n, int dim)
{
- int i;
-
- if (available(fp,vec,indent,title)) {
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s:\t",title);
- for(i=0; i<n; i++)
- fprintf(fp," %10g",vec[i]);
- (void) fprintf(fp,"\n");
- }
+ 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++)
+ {
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%5d]={", title, i);
+ for (j = 0; j < dim; j++)
+ {
+ if (j != 0)
+ {
+ (void) fprintf(fp, ", ");
+ }
+ (void) fprintf(fp, format, vec[i * dim + j]);
+ }
+ (void) fprintf(fp, "}\n");
+ }
+ }
}
-static void pr_int(FILE *fp,int indent,const char *title,int i)
+static void pr_int(FILE *fp, int indent, const char *title, int i)
{
- pr_indent(fp,indent);
- fprintf(fp,"%-20s = %d\n",title,i);
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %d\n", title, i);
}
-static void pr_gmx_large_int(FILE *fp,int indent,const char *title,gmx_large_int_t i)
+static void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i)
{
- char buf[STEPSTRSIZE];
+ char buf[STEPSTRSIZE];
- pr_indent(fp,indent);
- fprintf(fp,"%-20s = %s\n",title,gmx_step_str(i,buf));
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %s\n", title, gmx_step_str(i, buf));
}
-static void pr_real(FILE *fp,int indent,const char *title,real r)
+static void pr_real(FILE *fp, int indent, const char *title, real r)
{
- pr_indent(fp,indent);
- fprintf(fp,"%-20s = %g\n",title,r);
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %g\n", title, r);
}
-static void pr_double(FILE *fp,int indent,const char *title,double d)
+static void pr_double(FILE *fp, int indent, const char *title, double d)
{
- pr_indent(fp,indent);
- fprintf(fp,"%-20s = %g\n",title,d);
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %g\n", title, d);
}
-static void pr_str(FILE *fp,int indent,const char *title,const char *s)
+static void pr_str(FILE *fp, int indent, const char *title, const char *s)
{
- pr_indent(fp,indent);
- fprintf(fp,"%-20s = %s\n",title,s);
+ pr_indent(fp, indent);
+ fprintf(fp, "%-30s = %s\n", title, s);
}
-void pr_qm_opts(FILE *fp,int indent,const char *title,t_grpopts *opts)
+void pr_qm_opts(FILE *fp, int indent, const char *title, t_grpopts *opts)
{
- int i,m,j;
-
- 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,"bSH",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_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);
- }
+ int i, m, j;
+
+ 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,t_grpopts *opts,
- gmx_bool bMDPformat)
+static void pr_grp_opts(FILE *out, int indent, const char *title, 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,"anneal%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 ? " = " : ":");
- 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,"ann. times [%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);
- 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);
+ 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,rvec *m,
- gmx_bool bMDPformat)
+static void pr_matrix(FILE *fp, int indent, const char *title, 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);
+ 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,t_cosines *cos,
- gmx_bool bMDPformat)
+static void pr_cosine(FILE *fp, int indent, const char *title, 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);
- (void) pr_indent(fp,indent);
- fprintf(fp,"n = %d\n",cos->n);
- if (cos->n > 0) {
- (void) pr_indent(fp,indent+2);
- fprintf(fp,"a =");
- for(j=0; (j<cos->n); j++)
- fprintf(fp," %e",cos->a[j]);
- fprintf(fp,"\n");
- (void) pr_indent(fp,indent+2);
- fprintf(fp,"phi =");
- for(j=0; (j<cos->n); j++)
- fprintf(fp," %e",cos->phi[j]);
- fprintf(fp,"\n");
- }
- }
+ int j;
+
+ if (bMDPformat)
+ {
+ fprintf(fp, "%s = %d\n", title, cos->n);
+ }
+ else
+ {
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "n = %d\n", cos->n);
+ if (cos->n > 0)
+ {
+ (void) pr_indent(fp, indent+2);
+ fprintf(fp, "a =");
+ for (j = 0; (j < cos->n); j++)
+ {
+ fprintf(fp, " %e", cos->a[j]);
+ }
+ fprintf(fp, "\n");
+ (void) 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_gmx_large_int(fp,indent,t,s)
-#define PR(t,s) pr_real(fp,indent,t,s)
-#define PD(t,s) pr_double(fp,indent,t,s)
+#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, 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_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
+static void pr_pull_coord(FILE *fp, int indent, int c, t_pull_coord *pcrd)
{
- pr_indent(fp,indent);
- fprintf(fp,"pull-group %d:\n",g);
- indent += 2;
- pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
- pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
- PI("pbcatom",pg->pbcatom);
- pr_rvec(fp,indent,"vec",pg->vec,DIM,TRUE);
- pr_rvec(fp,indent,"init",pg->init,DIM,TRUE);
- PR("rate",pg->rate);
- PR("k",pg->k);
- PR("kB",pg->kB);
+ pr_indent(fp, indent);
+ fprintf(fp, "pull-coord %d:\n", c);
+ PI("group[0]", pcrd->group[0]);
+ PI("group[1]", pcrd->group[1]);
+ pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
+ pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
+ PR("init", pcrd->init);
+ PR("rate", pcrd->rate);
+ PR("k", pcrd->k);
+ PR("kB", pcrd->kB);
}
-static void pr_simtempvals(FILE *fp,int indent,t_simtemp *simtemp, int n_lambda, gmx_bool bMDPformat)
+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_rvec(fp,indent,"simulated tempering temperatures",simtemp->temperatures,n_lambda,TRUE);
+ 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,t_expanded *expand, int n_lambda, gmx_bool bMDPformat)
+static void pr_expandedvals(FILE *fp, int indent, t_expanded *expand, int n_lambda)
{
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-weights-equil",elmceq_names[expand->elmceq]);
+ 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);
+ PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
}
if (expand->elmceq == elmceqSAMPLES)
{
- PI("weight-equil-number-samples",expand->equil_samples);
+ PI("weight-equil-number-samples", expand->equil_samples);
}
if (expand->elmceq == elmceqSTEPS)
{
- PI("weight-equil-number-steps",expand->equil_steps);
+ PI("weight-equil-number-steps", expand->equil_steps);
}
if (expand->elmceq == elmceqWLDELTA)
{
- PR("weight-equil-wl-delta",expand->equil_wl_delta);
+ PR("weight-equil-wl-delta", expand->equil_wl_delta);
}
if (expand->elmceq == elmceqRATIO)
{
- PR("weight-equil-count-ratio",expand->equil_ratio);
+ PR("weight-equil-count-ratio", expand->equil_ratio);
}
-
- 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));
+ 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,t_lambda *fep, gmx_bool bMDPformat)
+static void pr_fepvals(FILE *fp, int indent, t_lambda *fep, gmx_bool bMDPformat)
{
- int i,j;
+ 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);
- PI("nstdhdl",fep->nstdhdl);
- PI("init-lambda-state",fep->init_fep_state);
- PR("init-lambda",fep->init_lambda);
- PR("delta-lambda",fep->delta_lambda);
if (!bMDPformat)
{
- PI("n-lambdas",fep->n_lambda);
+ PI("n-lambdas", fep->n_lambda);
}
if (fep->n_lambda > 0)
{
- pr_indent(fp,indent);
- 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++)
+ 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," %10g",fep->all_lambda[i][j]);
+ fprintf(fp, " TRUE");
}
- fprintf(fp,"\n");
+ 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");
}
}
-
- 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));
+ 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,t_pull *pull)
+static void pr_pull(FILE *fp, int indent, t_pull *pull)
{
- int g;
-
- PS("pull-geometry",EPULLGEOM(pull->eGeom));
- pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
- PR("pull-r1",pull->cyl_r1);
- PR("pull-r0",pull->cyl_r0);
- PR("pull-constr-tol",pull->constr_tol);
- PI("pull-nstxout",pull->nstxout);
- PI("pull-nstfout",pull->nstfout);
- PI("pull-ngrp",pull->ngrp);
- for(g=0; g<pull->ngrp+1; g++)
- pr_pullgrp(fp,indent,g,&pull->grp[g]);
+ int g;
+
+ PS("pull-geometry", EPULLGEOM(pull->eGeom));
+ pr_ivec(fp, indent, "pull-dim", pull->dim, DIM, TRUE);
+ PR("pull-r1", pull->cyl_r1);
+ PR("pull-r0", pull->cyl_r0);
+ PR("pull-constr-tol", pull->constr_tol);
+ PS("pull-print-reference", EBOOL(pull->bPrintRef));
+ 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,t_rotgrp *rotg)
+static void pr_rotgrp(FILE *fp, int indent, int g, t_rotgrp *rotg)
{
- pr_indent(fp,indent);
- fprintf(fp,"rotation_group %d:\n",g);
- indent += 2;
- PS("type",EROTGEOM(rotg->eType));
- PS("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_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,t_rot *rot)
+static void pr_rot(FILE *fp, int indent, t_rot *rot)
{
- int g;
+ 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, t_swapcoords *swap)
+{
+ int i, j;
+ char str[STRLEN];
+
+
+ PI("swap-frequency", swap->nstswap);
+ for (j = 0; j < 2; 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-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);
+}
+
- PI("rot_nstrout",rot->nstrout);
- PI("rot_nstsout",rot->nstsout);
- PI("rot_ngrp",rot->ngrp);
- for(g=0; g<rot->ngrp; g++)
- pr_rotgrp(fp,indent,g,&rot->grp[g]);
+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);
}
-void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
+
+void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir,
gmx_bool bMDPformat)
{
- const char *infbuf="inf";
- int i;
-
- if (available(fp,ir,indent,title)) {
- if (!bMDPformat)
- indent=pr_title(fp,indent,title);
- PS("integrator",EI(ir->eI));
- 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);
- PS("comm-mode",ECOM(ir->comm_mode));
- PI("nstlog",ir->nstlog);
- PI("nstxout",ir->nstxout);
- PI("nstvout",ir->nstvout);
- PI("nstfout",ir->nstfout);
- PI("nstcalcenergy",ir->nstcalcenergy);
- PI("nstenergy",ir->nstenergy);
- PI("nstxtcout",ir->nstxtcout);
- PR("init-t",ir->init_t);
- PR("delta-t",ir->delta_t);
-
- PR("xtcprec",ir->xtcprec);
- 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-geometry",ir->ewald_geometry);
- PR("epsilon-surface",ir->epsilon_surface);
- PS("optimize-fft",EBOOL(ir->bOptFFT));
- 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);
- PR("verlet-buffer-drift",ir->verletbuf_drift);
- PR("rlist",ir->rlist);
- PR("rlistlong",ir->rlistlong);
- PR("nstcalclr",ir->nstcalclr);
- PR("rtpi",ir->rtpi);
- 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);
- else
- PS("epsilon-r",infbuf);
- if (ir->epsilon_rf != 0)
- PR("epsilon-rf",ir->epsilon_rf);
- else
- PS("epsilon-rf",infbuf);
- PR("tabext",ir->tabext);
- PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
- 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-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->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,bMDPformat);
- }
- 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,bMDPformat);
- }
-
- PI("nwall",ir->nwall);
- PS("wall-type",EWALLTYPE(ir->wall_type));
- PI("wall-atomtype[0]",ir->wall_atomtype[0]);
- PI("wall-atomtype[1]",ir->wall_atomtype[1]);
- PR("wall-density[0]",ir->wall_density[0]);
- PR("wall-density[1]",ir->wall_density[1]);
- PR("wall-ewald-zfac",ir->wall_ewald_zfac);
-
- PS("pull",EPULLTYPE(ir->ePull));
- if (ir->ePull != epullNO)
- pr_pull(fp,indent,ir->pull);
-
- PS("rotation",EBOOL(ir->bRot));
- if (ir->bRot)
- pr_rot(fp,indent,ir->rot);
-
- 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("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);
-
- 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);
- pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
-
- PS("adress",EBOOL(ir->bAdress));
- if (ir->bAdress){
- PS("adress_type",EADRESSTYPE(ir->adress->type));
- PR("adress_const_wf",ir->adress->const_wf);
- PR("adress_ex_width",ir->adress->ex_width);
- PR("adress_hy_width",ir->adress->hy_width);
- 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);
- }
- 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);
- 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("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));
- }
+ const char *infbuf = "inf";
+ int i;
+
+ 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(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);
+
+ /* 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->gb_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", 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("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);
+ }
+
+ /* AdResS PARAMETERS */
+ PS("adress", EBOOL(ir->bAdress));
+ if (ir->bAdress)
+ {
+ PS("adress-type", EADRESSTYPE(ir->adress->type));
+ 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_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);
+ 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
-static void pr_harm(FILE *fp,t_iparams *iparams,const char *r,const char *kr)
+static void pr_harm(FILE *fp, t_iparams *iparams, const char *r, const char *kr)
{
- fprintf(fp,"%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
- r,iparams->harmonic.rA,kr,iparams->harmonic.krA,
- r,iparams->harmonic.rB,kr,iparams->harmonic.krB);
+ fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
+ r, iparams->harmonic.rA, kr, iparams->harmonic.krA,
+ r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
}
-void pr_iparams(FILE *fp,t_functype ftype,t_iparams *iparams)
+void pr_iparams(FILE *fp, t_functype ftype, t_iparams *iparams)
{
- int i;
- real VA[4],VB[4],*rbcA,*rbcB;
-
- switch (ftype) {
- case F_ANGLES:
- case F_G96ANGLES:
- pr_harm(fp,iparams,"th","ct");
- break;
- case F_CROSS_BOND_BONDS:
- fprintf(fp,"r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
- iparams->cross_bb.r1e,iparams->cross_bb.r2e,
- iparams->cross_bb.krr);
- break;
- case F_CROSS_BOND_ANGLES:
- fprintf(fp,"r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
- iparams->cross_ba.r1e,iparams->cross_ba.r2e,
- iparams->cross_ba.r3e,iparams->cross_ba.krt);
- break;
- case F_LINEAR_ANGLES:
- fprintf(fp,"klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
- iparams->linangle.klinA,iparams->linangle.aA,
- iparams->linangle.klinB,iparams->linangle.aB);
- break;
- case F_UREY_BRADLEY:
- fprintf(fp,"thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n",iparams->u_b.thetaA,iparams->u_b.kthetaA,iparams->u_b.r13A,iparams->u_b.kUBA,iparams->u_b.thetaB,iparams->u_b.kthetaB,iparams->u_b.r13B,iparams->u_b.kUBB);
- break;
- case F_QUARTIC_ANGLES:
- fprintf(fp,"theta=%15.8e",iparams->qangle.theta);
- for(i=0; i<5; i++)
- fprintf(fp,", c%c=%15.8e",'0'+i,iparams->qangle.c[i]);
- fprintf(fp,"\n");
- break;
- case F_BHAM:
- fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
- iparams->bham.a,iparams->bham.b,iparams->bham.c);
- break;
- case F_BONDS:
- case F_G96BONDS:
- case F_HARMONIC:
- pr_harm(fp,iparams,"b0","cb");
- break;
- case F_IDIHS:
- pr_harm(fp,iparams,"xi","cx");
- break;
- case F_MORSE:
- fprintf(fp,"b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
- iparams->morse.b0A,iparams->morse.cbA,iparams->morse.betaA,
- iparams->morse.b0B,iparams->morse.cbB,iparams->morse.betaB);
- break;
- case F_CUBICBONDS:
- fprintf(fp,"b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
- iparams->cubic.b0,iparams->cubic.kb,iparams->cubic.kcub);
- break;
- case F_CONNBONDS:
- fprintf(fp,"\n");
- break;
- case F_FENEBONDS:
- fprintf(fp,"bm=%15.8e, kb=%15.8e\n",iparams->fene.bm,iparams->fene.kb);
- break;
- case F_RESTRBONDS:
- fprintf(fp,"lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
- iparams->restraint.lowA,iparams->restraint.up1A,
- iparams->restraint.up2A,iparams->restraint.kA,
- iparams->restraint.lowB,iparams->restraint.up1B,
- iparams->restraint.up2B,iparams->restraint.kB);
- break;
- case F_TABBONDS:
- case F_TABBONDSNC:
- case F_TABANGLES:
- case F_TABDIHS:
- fprintf(fp,"tab=%d, kA=%15.8e, kB=%15.8e\n",
- iparams->tab.table,iparams->tab.kA,iparams->tab.kB);
- break;
- case F_POLARIZATION:
- fprintf(fp,"alpha=%15.8e\n",iparams->polarize.alpha);
- break;
- case F_ANHARM_POL:
- fprintf(fp,"alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
- iparams->anharm_polarize.alpha,
- iparams->anharm_polarize.drcut,
- iparams->anharm_polarize.khyp);
- break;
- case F_THOLE_POL:
- fprintf(fp,"a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
- iparams->thole.a,iparams->thole.alpha1,iparams->thole.alpha2,
- iparams->thole.rfac);
- break;
- case F_WATER_POL:
- fprintf(fp,"al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
- iparams->wpol.al_x,iparams->wpol.al_y,iparams->wpol.al_z,
- iparams->wpol.rOH,iparams->wpol.rHH,iparams->wpol.rOD);
- break;
- case F_LJ:
- fprintf(fp,"c6=%15.8e, c12=%15.8e\n",iparams->lj.c6,iparams->lj.c12);
- break;
- case F_LJ14:
- fprintf(fp,"c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
- iparams->lj14.c6A,iparams->lj14.c12A,
- iparams->lj14.c6B,iparams->lj14.c12B);
- break;
- case F_LJC14_Q:
- fprintf(fp,"fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
- iparams->ljc14.fqq,
- iparams->ljc14.qi,iparams->ljc14.qj,
- iparams->ljc14.c6,iparams->ljc14.c12);
- break;
- case F_LJC_PAIRS_NB:
- fprintf(fp,"qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
- iparams->ljcnb.qi,iparams->ljcnb.qj,
- iparams->ljcnb.c6,iparams->ljcnb.c12);
- break;
- case F_PDIHS:
- case F_PIDIHS:
- case F_ANGRES:
- case F_ANGRESZ:
- fprintf(fp,"phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
- iparams->pdihs.phiA,iparams->pdihs.cpA,
- iparams->pdihs.phiB,iparams->pdihs.cpB,
- iparams->pdihs.mult);
- break;
- case F_DISRES:
- fprintf(fp,"label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
- iparams->disres.label,iparams->disres.type,
- iparams->disres.low,iparams->disres.up1,
- iparams->disres.up2,iparams->disres.kfac);
- break;
- case F_ORIRES:
- fprintf(fp,"ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
- iparams->orires.ex,iparams->orires.label,iparams->orires.power,
- iparams->orires.c,iparams->orires.obs,iparams->orires.kfac);
- break;
- case F_DIHRES:
- fprintf(fp,"phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
- iparams->dihres.phiA,iparams->dihres.dphiA,iparams->dihres.kfacA,
- iparams->dihres.phiB,iparams->dihres.dphiB,iparams->dihres.kfacB);
- break;
- case F_POSRES:
- fprintf(fp,"pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
- iparams->posres.pos0A[XX],iparams->posres.pos0A[YY],
- iparams->posres.pos0A[ZZ],iparams->posres.fcA[XX],
- iparams->posres.fcA[YY],iparams->posres.fcA[ZZ],
- iparams->posres.pos0B[XX],iparams->posres.pos0B[YY],
- iparams->posres.pos0B[ZZ],iparams->posres.fcB[XX],
- iparams->posres.fcB[YY],iparams->posres.fcB[ZZ]);
- break;
- case F_FBPOSRES:
- fprintf(fp,"pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
- iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY],
- iparams->fbposres.pos0[ZZ], iparams->fbposres.geom,
- iparams->fbposres.r, iparams->fbposres.k);
- break;
- case F_RBDIHS:
- for (i=0; i<NR_RBDIHS; i++)
- fprintf(fp,"%srbcA[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcA[i]);
- fprintf(fp,"\n");
- for (i=0; i<NR_RBDIHS; i++)
- fprintf(fp,"%srbcB[%d]=%15.8e",i==0?"":", ",i,iparams->rbdihs.rbcB[i]);
- fprintf(fp,"\n");
- break;
- case F_FOURDIHS:
- /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
- * OPLS potential constants back.
- */
- rbcA = iparams->rbdihs.rbcA;
- rbcB = iparams->rbdihs.rbcB;
-
- VA[3] = -0.25*rbcA[4];
- VA[2] = -0.5*rbcA[3];
- VA[1] = 4.0*VA[3]-rbcA[2];
- VA[0] = 3.0*VA[2]-2.0*rbcA[1];
-
- VB[3] = -0.25*rbcB[4];
- VB[2] = -0.5*rbcB[3];
- VB[1] = 4.0*VB[3]-rbcB[2];
- VB[0] = 3.0*VB[2]-2.0*rbcB[1];
-
- for (i=0; i<NR_FOURDIHS; i++)
- fprintf(fp,"%sFourA[%d]=%15.8e",i==0?"":", ",i,VA[i]);
- fprintf(fp,"\n");
- for (i=0; i<NR_FOURDIHS; i++)
- fprintf(fp,"%sFourB[%d]=%15.8e",i==0?"":", ",i,VB[i]);
- fprintf(fp,"\n");
- break;
-
- case F_CONSTR:
- case F_CONSTRNC:
- fprintf(fp,"dA=%15.8e, dB=%15.8e\n",iparams->constr.dA,iparams->constr.dB);
- break;
- case F_SETTLE:
- fprintf(fp,"doh=%15.8e, dhh=%15.8e\n",iparams->settle.doh,
- iparams->settle.dhh);
- break;
- case F_VSITE2:
- fprintf(fp,"a=%15.8e\n",iparams->vsite.a);
- break;
- case F_VSITE3:
- case F_VSITE3FD:
- case F_VSITE3FAD:
- fprintf(fp,"a=%15.8e, b=%15.8e\n",iparams->vsite.a,iparams->vsite.b);
- break;
- case F_VSITE3OUT:
- case F_VSITE4FD:
- case F_VSITE4FDN:
- fprintf(fp,"a=%15.8e, b=%15.8e, c=%15.8e\n",
- iparams->vsite.a,iparams->vsite.b,iparams->vsite.c);
- break;
- case F_VSITEN:
- fprintf(fp,"n=%2d, a=%15.8e\n",iparams->vsiten.n,iparams->vsiten.a);
- break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n",iparams->gb.sar,iparams->gb.st,iparams->gb.pi,iparams->gb.gbr,iparams->gb.bmlt);
- break;
- case F_CMAP:
- fprintf(fp, "cmapA=%1d, cmapB=%1d\n",iparams->cmap.cmapA, iparams->cmap.cmapB);
- break;
- default:
- gmx_fatal(FARGS,"unknown function type %d (%s) in %s line %d",
- ftype,interaction_function[ftype].name,__FILE__,__LINE__);
- }
+ int i;
+ real VA[4], VB[4], *rbcA, *rbcB;
+
+ switch (ftype)
+ {
+ case F_ANGLES:
+ case F_G96ANGLES:
+ pr_harm(fp, iparams, "th", "ct");
+ break;
+ case F_CROSS_BOND_BONDS:
+ fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
+ iparams->cross_bb.r1e, iparams->cross_bb.r2e,
+ iparams->cross_bb.krr);
+ break;
+ case F_CROSS_BOND_ANGLES:
+ fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
+ iparams->cross_ba.r1e, iparams->cross_ba.r2e,
+ iparams->cross_ba.r3e, iparams->cross_ba.krt);
+ break;
+ case F_LINEAR_ANGLES:
+ fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
+ iparams->linangle.klinA, iparams->linangle.aA,
+ iparams->linangle.klinB, iparams->linangle.aB);
+ break;
+ case F_UREY_BRADLEY:
+ fprintf(fp, "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n", iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA, iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
+ break;
+ case F_QUARTIC_ANGLES:
+ fprintf(fp, "theta=%15.8e", iparams->qangle.theta);
+ for (i = 0; i < 5; i++)
+ {
+ fprintf(fp, ", c%c=%15.8e", '0'+i, iparams->qangle.c[i]);
+ }
+ fprintf(fp, "\n");
+ break;
+ case F_BHAM:
+ fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
+ iparams->bham.a, iparams->bham.b, iparams->bham.c);
+ break;
+ case F_BONDS:
+ case F_G96BONDS:
+ case F_HARMONIC:
+ pr_harm(fp, iparams, "b0", "cb");
+ break;
+ case F_IDIHS:
+ pr_harm(fp, iparams, "xi", "cx");
+ break;
+ case F_MORSE:
+ fprintf(fp, "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
+ iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
+ iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
+ break;
+ case F_CUBICBONDS:
+ fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
+ iparams->cubic.b0, iparams->cubic.kb, iparams->cubic.kcub);
+ break;
+ case F_CONNBONDS:
+ fprintf(fp, "\n");
+ break;
+ case F_FENEBONDS:
+ fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
+ break;
+ case F_RESTRBONDS:
+ fprintf(fp, "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
+ iparams->restraint.lowA, iparams->restraint.up1A,
+ iparams->restraint.up2A, iparams->restraint.kA,
+ iparams->restraint.lowB, iparams->restraint.up1B,
+ iparams->restraint.up2B, iparams->restraint.kB);
+ break;
+ case F_TABBONDS:
+ case F_TABBONDSNC:
+ case F_TABANGLES:
+ case F_TABDIHS:
+ fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n",
+ iparams->tab.table, iparams->tab.kA, iparams->tab.kB);
+ break;
+ case F_POLARIZATION:
+ fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
+ break;
+ case F_ANHARM_POL:
+ fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
+ iparams->anharm_polarize.alpha,
+ iparams->anharm_polarize.drcut,
+ iparams->anharm_polarize.khyp);
+ break;
+ case F_THOLE_POL:
+ fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
+ iparams->thole.a, iparams->thole.alpha1, iparams->thole.alpha2,
+ iparams->thole.rfac);
+ break;
+ case F_WATER_POL:
+ fprintf(fp, "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
+ iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z,
+ iparams->wpol.rOH, iparams->wpol.rHH, iparams->wpol.rOD);
+ break;
+ case F_LJ:
+ fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12);
+ break;
+ case F_LJ14:
+ fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
+ iparams->lj14.c6A, iparams->lj14.c12A,
+ iparams->lj14.c6B, iparams->lj14.c12B);
+ break;
+ case F_LJC14_Q:
+ fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
+ iparams->ljc14.fqq,
+ iparams->ljc14.qi, iparams->ljc14.qj,
+ iparams->ljc14.c6, iparams->ljc14.c12);
+ break;
+ case F_LJC_PAIRS_NB:
+ fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
+ iparams->ljcnb.qi, iparams->ljcnb.qj,
+ iparams->ljcnb.c6, iparams->ljcnb.c12);
+ break;
+ case F_PDIHS:
+ case F_PIDIHS:
+ case F_ANGRES:
+ case F_ANGRESZ:
+ fprintf(fp, "phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
+ iparams->pdihs.phiA, iparams->pdihs.cpA,
+ iparams->pdihs.phiB, iparams->pdihs.cpB,
+ iparams->pdihs.mult);
+ break;
+ case F_DISRES:
+ fprintf(fp, "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
+ iparams->disres.label, iparams->disres.type,
+ iparams->disres.low, iparams->disres.up1,
+ iparams->disres.up2, iparams->disres.kfac);
+ break;
+ case F_ORIRES:
+ fprintf(fp, "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
+ iparams->orires.ex, iparams->orires.label, iparams->orires.power,
+ iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
+ break;
+ case F_DIHRES:
+ fprintf(fp, "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
+ iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
+ iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
+ break;
+ case F_POSRES:
+ fprintf(fp, "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
+ iparams->posres.pos0A[XX], iparams->posres.pos0A[YY],
+ iparams->posres.pos0A[ZZ], iparams->posres.fcA[XX],
+ iparams->posres.fcA[YY], iparams->posres.fcA[ZZ],
+ iparams->posres.pos0B[XX], iparams->posres.pos0B[YY],
+ iparams->posres.pos0B[ZZ], iparams->posres.fcB[XX],
+ iparams->posres.fcB[YY], iparams->posres.fcB[ZZ]);
+ break;
+ case F_FBPOSRES:
+ fprintf(fp, "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
+ iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY],
+ iparams->fbposres.pos0[ZZ], iparams->fbposres.geom,
+ iparams->fbposres.r, iparams->fbposres.k);
+ break;
+ case F_RBDIHS:
+ for (i = 0; i < NR_RBDIHS; i++)
+ {
+ fprintf(fp, "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcA[i]);
+ }
+ fprintf(fp, "\n");
+ for (i = 0; i < NR_RBDIHS; i++)
+ {
+ fprintf(fp, "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcB[i]);
+ }
+ fprintf(fp, "\n");
+ break;
+ case F_FOURDIHS:
+ /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
+ * OPLS potential constants back.
+ */
+ rbcA = iparams->rbdihs.rbcA;
+ rbcB = iparams->rbdihs.rbcB;
+
+ VA[3] = -0.25*rbcA[4];
+ VA[2] = -0.5*rbcA[3];
+ VA[1] = 4.0*VA[3]-rbcA[2];
+ VA[0] = 3.0*VA[2]-2.0*rbcA[1];
+
+ VB[3] = -0.25*rbcB[4];
+ VB[2] = -0.5*rbcB[3];
+ VB[1] = 4.0*VB[3]-rbcB[2];
+ VB[0] = 3.0*VB[2]-2.0*rbcB[1];
+
+ for (i = 0; i < NR_FOURDIHS; i++)
+ {
+ fprintf(fp, "%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
+ }
+ fprintf(fp, "\n");
+ for (i = 0; i < NR_FOURDIHS; i++)
+ {
+ fprintf(fp, "%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
+ }
+ fprintf(fp, "\n");
+ break;
+
+ case F_CONSTR:
+ case F_CONSTRNC:
+ fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
+ break;
+ case F_SETTLE:
+ fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh,
+ iparams->settle.dhh);
+ break;
+ case F_VSITE2:
+ fprintf(fp, "a=%15.8e\n", iparams->vsite.a);
+ break;
+ case F_VSITE3:
+ case F_VSITE3FD:
+ case F_VSITE3FAD:
+ fprintf(fp, "a=%15.8e, b=%15.8e\n", iparams->vsite.a, iparams->vsite.b);
+ break;
+ case F_VSITE3OUT:
+ case F_VSITE4FD:
+ case F_VSITE4FDN:
+ fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
+ iparams->vsite.a, iparams->vsite.b, iparams->vsite.c);
+ break;
+ case F_VSITEN:
+ fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
+ break;
+ case F_GB12:
+ case F_GB13:
+ case F_GB14:
+ fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n", iparams->gb.sar, iparams->gb.st, iparams->gb.pi, iparams->gb.gbr, iparams->gb.bmlt);
+ break;
+ 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__);
+ }
}
-void pr_ilist(FILE *fp,int indent,const char *title,
- t_functype *functype,t_ilist *ilist, gmx_bool bShowNumbers)
+void pr_ilist(FILE *fp, int indent, const char *title,
+ t_functype *functype, t_ilist *ilist, gmx_bool bShowNumbers)
{
- int i,j,k,type,ftype;
+ int i, j, k, type, ftype;
t_iatom *iatoms;
-
- if (available(fp,ilist,indent,title) && ilist->nr > 0)
- {
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- fprintf(fp,"nr: %d\n",ilist->nr);
- if (ilist->nr > 0) {
- (void) pr_indent(fp,indent);
- fprintf(fp,"iatoms:\n");
- iatoms=ilist->iatoms;
- for (i=j=0; i<ilist->nr;) {
+
+ if (available(fp, ilist, indent, title) && ilist->nr > 0)
+ {
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "nr: %d\n", ilist->nr);
+ if (ilist->nr > 0)
+ {
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "iatoms:\n");
+ iatoms = ilist->iatoms;
+ for (i = j = 0; i < ilist->nr; )
+ {
#ifndef DEBUG
- (void) pr_indent(fp,indent+INDENT);
- type=*(iatoms++);
- ftype=functype[type];
- (void) fprintf(fp,"%d type=%d (%s)",
- bShowNumbers?j:-1,bShowNumbers?type:-1,
+ (void) pr_indent(fp, indent+INDENT);
+ type = *(iatoms++);
+ ftype = functype[type];
+ (void) fprintf(fp, "%d type=%d (%s)",
+ bShowNumbers ? j : -1, bShowNumbers ? type : -1,
interaction_function[ftype].name);
j++;
- for (k=0; k<interaction_function[ftype].nratoms; k++)
- (void) fprintf(fp," %u",*(iatoms++));
- (void) fprintf(fp,"\n");
- i+=1+interaction_function[ftype].nratoms;
+ for (k = 0; k < interaction_function[ftype].nratoms; k++)
+ {
+ (void) fprintf(fp, " %u", *(iatoms++));
+ }
+ (void) fprintf(fp, "\n");
+ i += 1+interaction_function[ftype].nratoms;
#else
- fprintf(fp,"%5d%5d\n",i,iatoms[i]);
+ fprintf(fp, "%5d%5d\n", i, iatoms[i]);
i++;
#endif
}
static void pr_cmap(FILE *fp, int indent, const char *title,
gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
{
- int i,j,nelem;
- real dx,idx;
-
+ int i, j, nelem;
+ real dx, idx;
+
dx = 360.0 / cmap_grid->grid_spacing;
nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
-
- if(available(fp,cmap_grid,indent,title))
+
+ if (available(fp, cmap_grid, indent, title))
{
- fprintf(fp,"%s\n",title);
-
- for(i=0;i<cmap_grid->ngrid;i++)
+ fprintf(fp, "%s\n", title);
+
+ for (i = 0; i < cmap_grid->ngrid; i++)
{
idx = -180.0;
- fprintf(fp,"%8s %8s %8s %8s\n","V","dVdx","dVdy","d2dV");
-
- fprintf(fp,"grid[%3d]={\n",bShowNumbers?i:-1);
-
- for(j=0;j<nelem;j++)
+ fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
+
+ fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
+
+ for (j = 0; j < nelem; j++)
{
- if( (j%cmap_grid->grid_spacing)==0)
+ if ( (j%cmap_grid->grid_spacing) == 0)
{
- fprintf(fp,"%8.1f\n",idx);
- idx+=dx;
+ fprintf(fp, "%8.1f\n", idx);
+ idx += dx;
}
-
- fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4]);
- fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+1]);
- fprintf(fp,"%8.3f ",cmap_grid->cmapdata[i].cmap[j*4+2]);
- fprintf(fp,"%8.3f\n",cmap_grid->cmapdata[i].cmap[j*4+3]);
+
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
+ fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
+ fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
}
- fprintf(fp,"\n");
+ fprintf(fp, "\n");
}
}
-
+
}
-void pr_ffparams(FILE *fp,int indent,const char *title,
+void pr_ffparams(FILE *fp, int indent, const char *title,
gmx_ffparams_t *ffparams,
gmx_bool bShowNumbers)
{
- int i,j;
-
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"atnr=%d\n",ffparams->atnr);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"ntypes=%d\n",ffparams->ntypes);
- for (i=0; i<ffparams->ntypes; i++) {
- (void) pr_indent(fp,indent+INDENT);
- (void) fprintf(fp,"functype[%d]=%s, ",
- bShowNumbers?i:-1,
- interaction_function[ffparams->functype[i]].name);
- pr_iparams(fp,ffparams->functype[i],&ffparams->iparams[i]);
- }
- (void) pr_double(fp,indent,"reppow",ffparams->reppow);
- (void) pr_real(fp,indent,"fudgeQQ",ffparams->fudgeQQ);
- pr_cmap(fp,indent,"cmap",&ffparams->cmap_grid,bShowNumbers);
+ int i, j;
+
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "atnr=%d\n", ffparams->atnr);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "ntypes=%d\n", ffparams->ntypes);
+ for (i = 0; i < ffparams->ntypes; i++)
+ {
+ (void) pr_indent(fp, indent+INDENT);
+ (void) fprintf(fp, "functype[%d]=%s, ",
+ bShowNumbers ? i : -1,
+ interaction_function[ffparams->functype[i]].name);
+ pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
+ }
+ (void) pr_double(fp, indent, "reppow", ffparams->reppow);
+ (void) pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
+ pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
}
-void pr_idef(FILE *fp,int indent,const char *title,t_idef *idef, gmx_bool bShowNumbers)
+void pr_idef(FILE *fp, int indent, const char *title, t_idef *idef, gmx_bool bShowNumbers)
{
- int i,j;
-
- if (available(fp,idef,indent,title)) {
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"atnr=%d\n",idef->atnr);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"ntypes=%d\n",idef->ntypes);
- for (i=0; i<idef->ntypes; i++) {
- (void) pr_indent(fp,indent+INDENT);
- (void) fprintf(fp,"functype[%d]=%s, ",
- bShowNumbers?i:-1,
- interaction_function[idef->functype[i]].name);
- pr_iparams(fp,idef->functype[i],&idef->iparams[i]);
- }
- (void) pr_real(fp,indent,"fudgeQQ",idef->fudgeQQ);
-
- for(j=0; (j<F_NRE); j++)
- pr_ilist(fp,indent,interaction_function[j].longname,
- idef->functype,&idef->il[j],bShowNumbers);
- }
+ int i, j;
+
+ if (available(fp, idef, indent, title))
+ {
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "atnr=%d\n", idef->atnr);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "ntypes=%d\n", idef->ntypes);
+ for (i = 0; i < idef->ntypes; i++)
+ {
+ (void) pr_indent(fp, indent+INDENT);
+ (void) fprintf(fp, "functype[%d]=%s, ",
+ bShowNumbers ? i : -1,
+ interaction_function[idef->functype[i]].name);
+ pr_iparams(fp, idef->functype[i], &idef->iparams[i]);
+ }
+ (void) pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
+
+ for (j = 0; (j < F_NRE); j++)
+ {
+ pr_ilist(fp, indent, interaction_function[j].longname,
+ idef->functype, &idef->il[j], bShowNumbers);
+ }
+ }
}
-static int pr_block_title(FILE *fp,int indent,const char *title,t_block *block)
+static int pr_block_title(FILE *fp, int indent, const char *title, t_block *block)
{
- int i;
+ int i;
- if (available(fp,block,indent,title))
+ if (available(fp, block, indent, title))
{
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"nr=%d\n",block->nr);
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "nr=%d\n", block->nr);
}
- return indent;
+ return indent;
}
-static int pr_blocka_title(FILE *fp,int indent,const char *title,t_blocka *block)
+static int pr_blocka_title(FILE *fp, int indent, const char *title, t_blocka *block)
{
- int i;
+ int i;
- if (available(fp,block,indent,title))
+ if (available(fp, block, indent, title))
{
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"nr=%d\n",block->nr);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"nra=%d\n",block->nra);
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "nr=%d\n", block->nr);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "nra=%d\n", block->nra);
}
- return indent;
+ return indent;
}
-static void low_pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block, gmx_bool bShowNumbers)
+static void low_pr_blocka(FILE *fp, int indent, const char *title, t_blocka *block, gmx_bool bShowNumbers)
{
- int i;
-
- if (available(fp,block,indent,title))
+ int i;
+
+ if (available(fp, block, indent, title))
{
- indent=pr_blocka_title(fp,indent,title,block);
- for (i=0; i<=block->nr; i++)
+ indent = pr_blocka_title(fp, indent, title, block);
+ for (i = 0; i <= block->nr; i++)
{
- (void) pr_indent(fp,indent+INDENT);
- (void) fprintf(fp,"%s->index[%d]=%u\n",
- title,bShowNumbers?i:-1,block->index[i]);
+ (void) pr_indent(fp, indent+INDENT);
+ (void) fprintf(fp, "%s->index[%d]=%d\n",
+ title, bShowNumbers ? i : -1, block->index[i]);
}
- for (i=0; i<block->nra; i++)
+ for (i = 0; i < block->nra; i++)
{
- (void) pr_indent(fp,indent+INDENT);
- (void) fprintf(fp,"%s->a[%d]=%u\n",
- title,bShowNumbers?i:-1,block->a[i]);
+ (void) pr_indent(fp, indent+INDENT);
+ (void) fprintf(fp, "%s->a[%d]=%d\n",
+ title, bShowNumbers ? i : -1, block->a[i]);
}
}
}
-void pr_block(FILE *fp,int indent,const char *title,t_block *block,gmx_bool bShowNumbers)
+void pr_block(FILE *fp, int indent, const char *title, t_block *block, gmx_bool bShowNumbers)
{
- int i,j,ok,size,start,end;
-
- if (available(fp,block,indent,title))
- {
- indent=pr_block_title(fp,indent,title,block);
- start=0;
- end=start;
- if ((ok=(block->index[start]==0))==0)
- (void) fprintf(fp,"block->index[%d] should be 0\n",start);
- else
- for (i=0; i<block->nr; i++)
- {
- end=block->index[i+1];
- size=pr_indent(fp,indent);
- if (end<=start)
- size+=fprintf(fp,"%s[%d]={}\n",title,i);
- else
- size+=fprintf(fp,"%s[%d]={%d..%d}\n",
- title,bShowNumbers?i:-1,
- bShowNumbers?start:-1,bShowNumbers?end-1:-1);
- start=end;
- }
+ int i, j, ok, size, start, end;
+
+ if (available(fp, block, indent, title))
+ {
+ indent = pr_block_title(fp, indent, title, block);
+ start = 0;
+ end = start;
+ if ((ok = (block->index[start] == 0)) == 0)
+ {
+ (void) fprintf(fp, "block->index[%d] should be 0\n", start);
+ }
+ else
+ {
+ for (i = 0; i < block->nr; i++)
+ {
+ end = block->index[i+1];
+ size = pr_indent(fp, indent);
+ if (end <= start)
+ {
+ size += fprintf(fp, "%s[%d]={}\n", title, i);
+ }
+ else
+ {
+ size += fprintf(fp, "%s[%d]={%d..%d}\n",
+ title, bShowNumbers ? i : -1,
+ bShowNumbers ? start : -1, bShowNumbers ? end-1 : -1);
+ }
+ start = end;
+ }
+ }
}
}
-void pr_blocka(FILE *fp,int indent,const char *title,t_blocka *block,gmx_bool bShowNumbers)
+void pr_blocka(FILE *fp, int indent, const char *title, t_blocka *block, gmx_bool bShowNumbers)
{
- int i,j,ok,size,start,end;
-
- if (available(fp,block,indent,title))
- {
- indent=pr_blocka_title(fp,indent,title,block);
- start=0;
- end=start;
- if ((ok=(block->index[start]==0))==0)
- (void) fprintf(fp,"block->index[%d] should be 0\n",start);
- else
- for (i=0; i<block->nr; i++)
- {
- end=block->index[i+1];
- size=pr_indent(fp,indent);
- if (end<=start)
- size+=fprintf(fp,"%s[%d]={",title,i);
- else
- size+=fprintf(fp,"%s[%d][%d..%d]={",
- title,bShowNumbers?i:-1,
- bShowNumbers?start:-1,bShowNumbers?end-1:-1);
- for (j=start; j<end; j++)
- {
- if (j>start) size+=fprintf(fp,", ");
- if ((size)>(USE_WIDTH))
- {
- (void) fprintf(fp,"\n");
- size=pr_indent(fp,indent+INDENT);
- }
- size+=fprintf(fp,"%u",block->a[j]);
- }
- (void) fprintf(fp,"}\n");
- start=end;
- }
- if ((end!=block->nra)||(!ok))
+ int i, j, ok, size, start, end;
+
+ if (available(fp, block, indent, title))
+ {
+ indent = pr_blocka_title(fp, indent, title, block);
+ start = 0;
+ end = start;
+ if ((ok = (block->index[start] == 0)) == 0)
+ {
+ (void) fprintf(fp, "block->index[%d] should be 0\n", start);
+ }
+ else
+ {
+ for (i = 0; i < block->nr; i++)
+ {
+ end = block->index[i+1];
+ size = pr_indent(fp, indent);
+ if (end <= start)
+ {
+ size += fprintf(fp, "%s[%d]={", title, i);
+ }
+ else
+ {
+ size += fprintf(fp, "%s[%d][%d..%d]={",
+ title, bShowNumbers ? i : -1,
+ bShowNumbers ? start : -1, bShowNumbers ? end-1 : -1);
+ }
+ for (j = start; j < end; j++)
+ {
+ if (j > start)
+ {
+ size += fprintf(fp, ", ");
+ }
+ if ((size) > (USE_WIDTH))
+ {
+ (void) fprintf(fp, "\n");
+ size = pr_indent(fp, indent+INDENT);
+ }
+ size += fprintf(fp, "%d", block->a[j]);
+ }
+ (void) fprintf(fp, "}\n");
+ start = end;
+ }
+ }
+ if ((end != block->nra) || (!ok))
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"tables inconsistent, dumping complete tables:\n");
- low_pr_blocka(fp,indent,title,block,bShowNumbers);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "tables inconsistent, dumping complete tables:\n");
+ low_pr_blocka(fp, indent, title, block, bShowNumbers);
}
}
}
-static void pr_strings(FILE *fp,int indent,const char *title,char ***nm,int n, gmx_bool bShowNumbers)
+static void pr_strings(FILE *fp, int indent, const char *title, char ***nm, int n, gmx_bool bShowNumbers)
{
- int i;
+ int i;
- if (available(fp,nm,indent,title))
- {
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++)
+ if (available(fp, nm, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]={name=\"%s\"}\n",
- title,bShowNumbers?i:-1,*(nm[i]));
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]={name=\"%s\"}\n",
+ title, bShowNumbers ? i : -1, *(nm[i]));
}
}
}
-static void pr_strings2(FILE *fp,int indent,const char *title,
- char ***nm,char ***nmB,int n, gmx_bool bShowNumbers)
+static void pr_strings2(FILE *fp, int indent, const char *title,
+ char ***nm, char ***nmB, int n, gmx_bool bShowNumbers)
{
- int i;
+ int i;
- if (available(fp,nm,indent,title))
- {
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++)
+ if (available(fp, nm, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
- title,bShowNumbers?i:-1,*(nm[i]),*(nmB[i]));
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
+ title, bShowNumbers ? i : -1, *(nm[i]), *(nmB[i]));
}
}
}
-static void pr_resinfo(FILE *fp,int indent,const char *title,t_resinfo *resinfo,int n, gmx_bool bShowNumbers)
+static void pr_resinfo(FILE *fp, int indent, const char *title, t_resinfo *resinfo, int n, gmx_bool bShowNumbers)
{
int i;
-
- if (available(fp,resinfo,indent,title))
- {
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++)
+
+ if (available(fp, resinfo, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
{
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
- title,bShowNumbers?i:-1,
- *(resinfo[i].name),resinfo[i].nr,
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
+ title, bShowNumbers ? i : -1,
+ *(resinfo[i].name), resinfo[i].nr,
(resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
}
}
}
-static void pr_atom(FILE *fp,int indent,const char *title,t_atom *atom,int n)
+static void pr_atom(FILE *fp, int indent, const char *title, t_atom *atom, int n)
{
- int i,j;
-
- if (available(fp,atom,indent,title)) {
- indent=pr_title_n(fp,indent,title,n);
- for (i=0; i<n; i++) {
- (void) pr_indent(fp,indent);
- fprintf(fp,"%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
- "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
- title,i,atom[i].type,atom[i].typeB,ptype_str[atom[i].ptype],
- atom[i].m,atom[i].q,atom[i].mB,atom[i].qB,
- atom[i].resind,atom[i].atomnumber);
- }
- }
+ int i, j;
+
+ if (available(fp, atom, indent, title))
+ {
+ indent = pr_title_n(fp, indent, title, n);
+ for (i = 0; i < n; i++)
+ {
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
+ "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
+ title, i, atom[i].type, atom[i].typeB, ptype_str[atom[i].ptype],
+ atom[i].m, atom[i].q, atom[i].mB, atom[i].qB,
+ atom[i].resind, atom[i].atomnumber);
+ }
+ }
}
-static void pr_grps(FILE *fp,int indent,const char *title,t_grps grps[],
- char **grpname[], gmx_bool bShowNumbers)
+static void pr_grps(FILE *fp, const char *title, t_grps grps[], char **grpname[])
{
- int i,j;
+ int i, j;
- for(i=0; (i<egcNR); i++)
+ for (i = 0; (i < egcNR); i++)
{
- fprintf(fp,"%s[%-12s] nr=%d, name=[",title,gtypes[i],grps[i].nr);
- for(j=0; (j<grps[i].nr); j++)
+ fprintf(fp, "%s[%-12s] nr=%d, name=[", title, gtypes[i], grps[i].nr);
+ for (j = 0; (j < grps[i].nr); j++)
{
- fprintf(fp," %s",*(grpname[grps[i].nm_ind[j]]));
+ fprintf(fp, " %s", *(grpname[grps[i].nm_ind[j]]));
}
- fprintf(fp,"]\n");
+ fprintf(fp, "]\n");
}
}
-static void pr_groups(FILE *fp,int indent,const char *title,
+static void pr_groups(FILE *fp, int indent,
gmx_groups_t *groups,
gmx_bool bShowNumbers)
{
int grpnr[egcNR];
- int nat_max,i,g;
+ int nat_max, i, g;
- pr_grps(fp,indent,"grp",groups->grps,groups->grpname,bShowNumbers);
- pr_strings(fp,indent,"grpname",groups->grpname,groups->ngrpname,bShowNumbers);
+ pr_grps(fp, "grp", groups->grps, groups->grpname);
+ pr_strings(fp, indent, "grpname", groups->grpname, groups->ngrpname, bShowNumbers);
- (void) pr_indent(fp,indent);
- fprintf(fp,"groups ");
- for(g=0; g<egcNR; g++)
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "groups ");
+ for (g = 0; g < egcNR; g++)
{
- printf(" %5.5s",gtypes[g]);
+ printf(" %5.5s", gtypes[g]);
}
printf("\n");
- (void) pr_indent(fp,indent);
- fprintf(fp,"allocated ");
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "allocated ");
nat_max = 0;
- for(g=0; g<egcNR; g++)
+ for (g = 0; g < egcNR; g++)
{
- printf(" %5d",groups->ngrpnr[g]);
- nat_max = max(nat_max,groups->ngrpnr[g]);
+ printf(" %5d", groups->ngrpnr[g]);
+ nat_max = max(nat_max, groups->ngrpnr[g]);
}
printf("\n");
if (nat_max == 0)
{
- (void) pr_indent(fp,indent);
- fprintf(fp,"groupnr[%5s] =","*");
- for(g=0; g<egcNR; g++)
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "groupnr[%5s] =", "*");
+ for (g = 0; g < egcNR; g++)
{
- fprintf(fp," %3d ",0);
+ fprintf(fp, " %3d ", 0);
}
- fprintf(fp,"\n");
+ fprintf(fp, "\n");
}
else
{
- for(i=0; i<nat_max; i++)
+ for (i = 0; i < nat_max; i++)
{
- (void) pr_indent(fp,indent);
- fprintf(fp,"groupnr[%5d] =",i);
- for(g=0; g<egcNR; g++)
+ (void) pr_indent(fp, indent);
+ fprintf(fp, "groupnr[%5d] =", i);
+ for (g = 0; g < egcNR; g++)
{
- fprintf(fp," %3d ",
+ fprintf(fp, " %3d ",
groups->grpnr[g] ? groups->grpnr[g][i] : 0);
}
- fprintf(fp,"\n");
+ fprintf(fp, "\n");
}
}
}
-void pr_atoms(FILE *fp,int indent,const char *title,t_atoms *atoms,
- gmx_bool bShownumbers)
+void pr_atoms(FILE *fp, int indent, const char *title, t_atoms *atoms,
+ gmx_bool bShownumbers)
{
- if (available(fp,atoms,indent,title))
+ if (available(fp, atoms, indent, title))
{
- indent=pr_title(fp,indent,title);
- pr_atom(fp,indent,"atom",atoms->atom,atoms->nr);
- pr_strings(fp,indent,"atom",atoms->atomname,atoms->nr,bShownumbers);
- pr_strings2(fp,indent,"type",atoms->atomtype,atoms->atomtypeB,atoms->nr,bShownumbers);
- pr_resinfo(fp,indent,"residue",atoms->resinfo,atoms->nres,bShownumbers);
+ indent = pr_title(fp, indent, title);
+ pr_atom(fp, indent, "atom", atoms->atom, atoms->nr);
+ pr_strings(fp, indent, "atom", atoms->atomname, atoms->nr, bShownumbers);
+ pr_strings2(fp, indent, "type", atoms->atomtype, atoms->atomtypeB, atoms->nr, bShownumbers);
+ pr_resinfo(fp, indent, "residue", atoms->resinfo, atoms->nres, bShownumbers);
}
}
-void pr_atomtypes(FILE *fp,int indent,const char *title,t_atomtypes *atomtypes,
- gmx_bool bShowNumbers)
+void pr_atomtypes(FILE *fp, int indent, const char *title, t_atomtypes *atomtypes,
+ gmx_bool bShowNumbers)
{
- int i;
- if (available(fp,atomtypes,indent,title))
- {
- indent=pr_title(fp,indent,title);
- for(i=0;i<atomtypes->nr;i++) {
- pr_indent(fp,indent);
- fprintf(fp,
- "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
- bShowNumbers?i:-1,atomtypes->radius[i],atomtypes->vol[i],
- atomtypes->gb_radius[i],
- atomtypes->surftens[i],atomtypes->atomnumber[i],atomtypes->S_hct[i]);
+ int i;
+ if (available(fp, atomtypes, indent, title))
+ {
+ indent = pr_title(fp, indent, title);
+ for (i = 0; i < atomtypes->nr; i++)
+ {
+ pr_indent(fp, indent);
+ fprintf(fp,
+ "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
+ bShowNumbers ? i : -1, atomtypes->radius[i], atomtypes->vol[i],
+ atomtypes->gb_radius[i],
+ atomtypes->surftens[i], atomtypes->atomnumber[i], atomtypes->S_hct[i]);
+ }
}
- }
}
-static void pr_moltype(FILE *fp,int indent,const char *title,
- gmx_moltype_t *molt,int n,
+static void pr_moltype(FILE *fp, int indent, const char *title,
+ gmx_moltype_t *molt, int n,
gmx_ffparams_t *ffparams,
gmx_bool bShowNumbers)
{
int j;
- indent = pr_title_n(fp,indent,title,n);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"name=\"%s\"\n",*(molt->name));
- pr_atoms(fp,indent,"atoms",&(molt->atoms),bShowNumbers);
- pr_block(fp,indent,"cgs",&molt->cgs, bShowNumbers);
- pr_blocka(fp,indent,"excls",&molt->excls, bShowNumbers);
- for(j=0; (j<F_NRE); j++) {
- pr_ilist(fp,indent,interaction_function[j].longname,
- ffparams->functype,&molt->ilist[j],bShowNumbers);
+ indent = pr_title_n(fp, indent, title, n);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "name=\"%s\"\n", *(molt->name));
+ pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
+ pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
+ pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
+ for (j = 0; (j < F_NRE); j++)
+ {
+ pr_ilist(fp, indent, interaction_function[j].longname,
+ ffparams->functype, &molt->ilist[j], bShowNumbers);
}
}
-static void pr_molblock(FILE *fp,int indent,const char *title,
- gmx_molblock_t *molb,int n,
- gmx_moltype_t *molt,
- gmx_bool bShowNumbers)
+static void pr_molblock(FILE *fp, int indent, const char *title,
+ gmx_molblock_t *molb, int n,
+ gmx_moltype_t *molt)
{
- indent = pr_title_n(fp,indent,title,n);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"%-20s = %d \"%s\"\n",
- "moltype",molb->type,*(molt[molb->type].name));
- pr_int(fp,indent,"#molecules",molb->nmol);
- pr_int(fp,indent,"#atoms_mol",molb->natoms_mol);
- pr_int(fp,indent,"#posres_xA",molb->nposres_xA);
- if (molb->nposres_xA > 0) {
- pr_rvecs(fp,indent,"posres_xA",molb->posres_xA,molb->nposres_xA);
- }
- pr_int(fp,indent,"#posres_xB",molb->nposres_xB);
- if (molb->nposres_xB > 0) {
- pr_rvecs(fp,indent,"posres_xB",molb->posres_xB,molb->nposres_xB);
+ indent = pr_title_n(fp, indent, title, n);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "%-20s = %d \"%s\"\n",
+ "moltype", molb->type, *(molt[molb->type].name));
+ pr_int(fp, indent, "#molecules", molb->nmol);
+ pr_int(fp, indent, "#atoms_mol", molb->natoms_mol);
+ pr_int(fp, indent, "#posres_xA", molb->nposres_xA);
+ if (molb->nposres_xA > 0)
+ {
+ pr_rvecs(fp, indent, "posres_xA", molb->posres_xA, molb->nposres_xA);
+ }
+ pr_int(fp, indent, "#posres_xB", molb->nposres_xB);
+ if (molb->nposres_xB > 0)
+ {
+ pr_rvecs(fp, indent, "posres_xB", molb->posres_xB, molb->nposres_xB);
}
}
-void pr_mtop(FILE *fp,int indent,const char *title,gmx_mtop_t *mtop,
+void pr_mtop(FILE *fp, int indent, const char *title, gmx_mtop_t *mtop,
gmx_bool bShowNumbers)
{
- int mt,mb;
-
- if (available(fp,mtop,indent,title)) {
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"name=\"%s\"\n",*(mtop->name));
- pr_int(fp,indent,"#atoms",mtop->natoms);
- pr_int(fp,indent,"#molblock",mtop->nmolblock);
- for(mb=0; mb<mtop->nmolblock; mb++) {
- pr_molblock(fp,indent,"molblock",&mtop->molblock[mb],mb,
- mtop->moltype,bShowNumbers);
+ int mt, mb;
+
+ if (available(fp, mtop, indent, title))
+ {
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "name=\"%s\"\n", *(mtop->name));
+ pr_int(fp, indent, "#atoms", mtop->natoms);
+ pr_int(fp, indent, "#molblock", mtop->nmolblock);
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
}
- pr_ffparams(fp,indent,"ffparams",&(mtop->ffparams),bShowNumbers);
- pr_atomtypes(fp,indent,"atomtypes",&(mtop->atomtypes),bShowNumbers);
- for(mt=0; mt<mtop->nmoltype; mt++) {
- pr_moltype(fp,indent,"moltype",&mtop->moltype[mt],mt,
- &mtop->ffparams,bShowNumbers);
+ pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
+ pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
+ &mtop->ffparams, bShowNumbers);
}
- pr_groups(fp,indent,"groups",&mtop->groups,bShowNumbers);
+ pr_groups(fp, indent, &mtop->groups, bShowNumbers);
}
}
-void pr_top(FILE *fp,int indent,const char *title,t_topology *top, gmx_bool bShowNumbers)
+void pr_top(FILE *fp, int indent, const char *title, t_topology *top, gmx_bool bShowNumbers)
{
- if (available(fp,top,indent,title)) {
- indent=pr_title(fp,indent,title);
- (void) pr_indent(fp,indent);
- (void) fprintf(fp,"name=\"%s\"\n",*(top->name));
- pr_atoms(fp,indent,"atoms",&(top->atoms),bShowNumbers);
- pr_atomtypes(fp,indent,"atomtypes",&(top->atomtypes),bShowNumbers);
- pr_block(fp,indent,"cgs",&top->cgs, bShowNumbers);
- pr_block(fp,indent,"mols",&top->mols, bShowNumbers);
- pr_blocka(fp,indent,"excls",&top->excls, bShowNumbers);
- pr_idef(fp,indent,"idef",&top->idef,bShowNumbers);
- }
+ if (available(fp, top, indent, title))
+ {
+ indent = pr_title(fp, indent, title);
+ (void) pr_indent(fp, indent);
+ (void) fprintf(fp, "name=\"%s\"\n", *(top->name));
+ pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
+ pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
+ pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
+ pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
+ pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
+ pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
+ }
}
-void pr_header(FILE *fp,int indent,const char *title,t_tpxheader *sh)
+void pr_header(FILE *fp, int indent, const char *title, t_tpxheader *sh)
{
- char buf[22];
-
- if (available(fp,sh,indent,title))
+ char buf[22];
+
+ if (available(fp, sh, indent, title))
{
- indent=pr_title(fp,indent,title);
- pr_indent(fp,indent);
- fprintf(fp,"bIr = %spresent\n",sh->bIr?"":"not ");
- pr_indent(fp,indent);
- fprintf(fp,"bBox = %spresent\n",sh->bBox?"":"not ");
- pr_indent(fp,indent);
- fprintf(fp,"bTop = %spresent\n",sh->bTop?"":"not ");
- pr_indent(fp,indent);
- fprintf(fp,"bX = %spresent\n",sh->bX?"":"not ");
- pr_indent(fp,indent);
- fprintf(fp,"bV = %spresent\n",sh->bV?"":"not ");
- pr_indent(fp,indent);
- fprintf(fp,"bF = %spresent\n",sh->bF?"":"not ");
-
- pr_indent(fp,indent);
- fprintf(fp,"natoms = %d\n",sh->natoms);
- pr_indent(fp,indent);
- fprintf(fp,"lambda = %e\n",sh->lambda);
+ indent = pr_title(fp, indent, title);
+ pr_indent(fp, indent);
+ fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
+ pr_indent(fp, indent);
+ fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
+ pr_indent(fp, indent);
+ fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
+ pr_indent(fp, indent);
+ fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
+ pr_indent(fp, indent);
+ fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
+ pr_indent(fp, indent);
+ fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
+
+ pr_indent(fp, indent);
+ fprintf(fp, "natoms = %d\n", sh->natoms);
+ pr_indent(fp, indent);
+ fprintf(fp, "lambda = %e\n", sh->lambda);
}
}
-void pr_commrec(FILE *fp,int indent,t_commrec *cr)
+void pr_commrec(FILE *fp, int indent, t_commrec *cr)
{
- pr_indent(fp,indent);
- fprintf(fp,"commrec:\n");
- indent+=2;
- pr_indent(fp,indent);
- fprintf(fp,"nodeid = %d\n",cr->nodeid);
- pr_indent(fp,indent);
- fprintf(fp,"nnodes = %d\n",cr->nnodes);
- pr_indent(fp,indent);
- fprintf(fp,"npmenodes = %d\n",cr->npmenodes);
- /*
- pr_indent(fp,indent);
- fprintf(fp,"threadid = %d\n",cr->threadid);
- pr_indent(fp,indent);
- fprintf(fp,"nthreads = %d\n",cr->nthreads);
- */
+ pr_indent(fp, indent);
+ fprintf(fp, "commrec:\n");
+ indent += 2;
+ pr_indent(fp, indent);
+ fprintf(fp, "rank = %d\n", cr->nodeid);
+ pr_indent(fp, indent);
+ fprintf(fp, "number of ranks = %d\n", cr->nnodes);
+ pr_indent(fp, indent);
+ fprintf(fp, "PME-only ranks = %d\n", cr->npmenodes);
+ /*
+ pr_indent(fp,indent);
+ fprintf(fp,"threadid = %d\n",cr->threadid);
+ pr_indent(fp,indent);
+ fprintf(fp,"nthreads = %d\n",cr->nthreads);
+ */
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff