Remove double declaration in headers

Change-Id: Ibaaee5b8bb8c6b3f4cf12c34efd2229f346a838f

diff --git a/include/confio.h b/include/confio.h
index a8238babc66c603e79b27bec7659759fed92115c..f0fbb9673b983d7e468b4eb972c2c2f4f24964df 100644 (file)
--- a/include/confio.h
+++ b/include/confio.h
@@ -46,10 +46,6 @@
 extern "C" {
 #endif
   
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
-/* allocate memory for the arrays, set nr to natoms and nres to 0
- * set pdbinfo to NULL or allocate memory for it */  
-
 int read_g96_conf(FILE *fp,const char *infile,t_trxframe *fr, char *line);
 /* read a Gromos96 coordinate or trajectory file,                       *
  * returns the number of atoms                                          *

diff --git a/include/maths.h b/include/maths.h
index 4a82797d3c2e2ec3bbf9040381c2dd9486dfb94c..e2c944bb04c78d1e827d0c3c1fa8298a61e8c8fe 100644 (file)
--- a/include/maths.h
+++ b/include/maths.h
@@ -99,8 +99,6 @@ static const double sy_const[MAX_SUZUKI_YOSHIDA_NUM+1][MAX_SUZUKI_YOSHIDA_NUM+1]
 int            gmx_nint(real a);
 real    sign(real x,real y);
 
-int            gmx_nint(real a);
-real    sign(real x,real y);
 real    cuberoot (real a);
 double  gmx_erfd(double x);
 double  gmx_erfcd(double x);

diff --git a/include/md_support.h b/include/md_support.h
index 7543ceaeba0278c747221c45f146508c36cdde9a..9e1a99330c0be701cc893c5b630773081675ffd0 100644 (file)
--- a/include/md_support.h
+++ b/include/md_support.h
@@ -127,21 +127,6 @@ void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inpu
                     int natoms, gmx_bool *bSumEkinhOld, int flags);
 /* Compute global variables during integration */
 
-void md_print_info(const t_commrec *cr, FILE *fplog,
-                   const char *fmt, ...);
-/* Print an general information message to stderr on the master node
- * and to fplog if fplog!=NULL.
- * fmt is a standard printf formatting string which should end in \n,
- * the arguments after that contain the values to be printed, as in printf.
- */
-
-void md_print_warn(const t_commrec *cr, FILE *fplog,
-                   const char *fmt, ...);
-/* As md_print_info above, but for important notices or warnings.
- * The only difference with md_print_info is that a newline is printed
- * before and after the message such that it stands out.
- */
-
 #ifdef __cplusplus
 }
 #endif

diff --git a/include/rdgroup.h b/include/rdgroup.h
deleted file mode 100644 (file)
index 5ac1865..0000000
--- a/include/rdgroup.h
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * 
- *                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
- * 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.
- * 
- * 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:
- * Gromacs Runs On Most of All Computer Systems
- */
-
-#ifndef _rdgroup_h
-#define _rdgroup_h
-
-#include "typedefs.h"
-
-#ifdef __cplusplus
-extern "C" { 
-#endif
-
-void check_index(char *gname,int n,atom_id index[],
-                       char *traj,int natoms);
-/* Checks if any index is smaller than zero or larger than natoms,
- * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
- * and traj (if traj=NULL, "the trajectory" is used).
- */
-
-void rd_index(const char *statfile,int ngrps,int isize[],
-             atom_id *index[],char *grpnames[]);
-/* Assume the group file is generated, so the
- * format need not be user-friendly. The format is:
- * nr of groups, total nr of atoms
- * for each group: name nr of element, elements
- * The function opens a file, reads ngrps groups, puts the
- * sizes in isize, the atom_id s in index and the names of
- * the groups in grpnames.
- *
- * It is also assumed, that when ngrps groups are requested
- * memory has been allocated for ngrps index arrays, and that
- * the dimension of the isize and grpnames arrays are ngrps.
- */
- 
-void rd_index_nrs(char *statfile,int ngrps,int isize[],
-                 atom_id *index[],char *grpnames[],int grpnr[]);
-/* the same but also reads the number of the selected group*/
-
-void get_index(t_atoms *atoms, const char *fnm, int ngrps,
-              int isize[], atom_id *index[],char *grpnames[]);
-/* Does the same as rd_index, but if the fnm pointer is NULL it
- * will not read from fnm, but it will make default index groups
- * for the atoms in *atoms.
- */ 
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _rdgroup_h */

diff --git a/include/toputil.h b/include/toputil.h
index f85bec1db5cef40bb6ffa1abcca0ea538716fc6a..f7260f4389957b983bd515e9d0bac2e00e1e6b95 100644 (file)
--- a/include/toputil.h
+++ b/include/toputil.h
@@ -66,12 +66,6 @@ void init_top  (t_topology *top);
 void done_top(t_topology *top);
 
 /* FREE */
-void done_block(t_block *block);
-
-void done_top(t_topology *top);
-
-void done_atom (t_atoms *at);
-
 void done_mi(t_molinfo *mi);
 
 /* PRINTING */

diff --git a/src/contrib/gmx_sdf.c b/src/contrib/gmx_sdf.c
index e5972af00a5194d5dd0c4699a6a694ac8081a2d7..0a44beb2e3c862ba9cda362293dc1095e0735e50 100644 (file)
--- a/src/contrib/gmx_sdf.c
+++ b/src/contrib/gmx_sdf.c
@@ -33,7 +33,7 @@
 #include "futil.h"
 #include "statutil.h"
 #include "tpxio.h"
-#include "rdgroup.h"
+#include "index.h"
 #include "smalloc.h"
 #include "nrnb.h"
 #include "gstat.h"

diff --git a/src/kernel/md.c b/src/kernel/md.c
index 4e05effd83d03479febec25a876ddc2979130348..5faa14445d090d96b19a4f4b15a614ef2a8416b4 100644 (file)
--- a/src/kernel/md.c
+++ b/src/kernel/md.c
@@ -54,6 +54,7 @@
 #include "xtcio.h"
 #include "mdrun.h"
 #include "md_support.h"
+#include "md_logging.h"
 #include "confio.h"
 #include "network.h"
 #include "pull.h"

diff --git a/src/kernel/readpull.c b/src/kernel/readpull.c
index 87a4d38992bdf038435807d300daca899bad3e8d..4523eed2d95cdfecc1b7e33457256fb34b6f9308 100644 (file)
--- a/src/kernel/readpull.c
+++ b/src/kernel/readpull.c
@@ -48,7 +48,7 @@
 #include "names.h"
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "rdgroup.h"
+#include "index.h"
 #include "symtab.h"
 #include "readinp.h"
 #include "readir.h"

diff --git a/src/mdlib/forcerec.c b/src/mdlib/forcerec.c
index 895832873eb87a7e1154a6c1bbdf1ec52dc58ed8..09af686f8e46562e1c2a2284924c0942670b9cf3 100644 (file)
--- a/src/mdlib/forcerec.c
+++ b/src/mdlib/forcerec.c
@@ -62,6 +62,7 @@
 #include "txtdump.h"
 #include "coulomb.h"
 #include "md_support.h"
+#include "md_logging.h"
 #include "domdec.h"
 #include "partdec.h"
 #include "qmmm.h"

diff --git a/src/mdlib/iteratedconstraints.c b/src/mdlib/iteratedconstraints.c
index 6a4a21532f7bbcb620867a16981d983885d2fbc6..33851e0bd310b978555137e61006b4e6dd6bb7df 100644 (file)
--- a/src/mdlib/iteratedconstraints.c
+++ b/src/mdlib/iteratedconstraints.c
@@ -42,6 +42,7 @@
 #include "gmx_fatal.h"
 #include "mdrun.h"
 #include "md_support.h"
+#include "md_logging.h"
 #include "types/iteratedconstraints.h"
 
 #ifdef GMX_DOUBLE

diff --git a/src/mdlib/pull.c b/src/mdlib/pull.c
index 173a245a1a5f2afaaee641a7eb21b88e1d6535c4..b0512efafde2f7f340d4a727ea81df738c86f861 100644 (file)
--- a/src/mdlib/pull.c
+++ b/src/mdlib/pull.c
@@ -42,7 +42,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include "futil.h"
-#include "rdgroup.h"
+#include "index.h"
 #include "statutil.h"
 #include "gmxfio.h"
 #include "vec.h" 

diff --git a/src/mdlib/pullutil.c b/src/mdlib/pullutil.c
index 1d192a5ecfabfdc73398882d09d4cab2ade7d749..43fc0434dd6b1f51bb5841bd2d1b72bc6c2d07e2 100644 (file)
--- a/src/mdlib/pullutil.c
+++ b/src/mdlib/pullutil.c
@@ -48,7 +48,6 @@
 #include "names.h"
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "rdgroup.h"
 #include "symtab.h"
 #include "index.h"
 #include "confio.h"

diff --git a/src/tools/make_edi.c b/src/tools/make_edi.c
index 1a9b9ef622a1c860730b7c092047661aa9cd06e2..dfbbd42295bc7f0db71b3a02f261871f0e4b6c31 100644 (file)
--- a/src/tools/make_edi.c
+++ b/src/tools/make_edi.c
@@ -52,7 +52,6 @@
 #include "copyrite.h"
 #include "futil.h"
 #include "statutil.h"
-#include "rdgroup.h"
 #include "pdbio.h"
 #include "confio.h"
 #include "tpxio.h"