Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_dos.c

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 13f26dcf4022fe36478eca22409c4bfb87791d75..e353d7a3e87c0b475ceceea777ebc2494ffb9f22 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -1,61 +1,59 @@
-/* -*- 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
+ * Copyright (c) 2011,2012,2013,2014, 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.
  *
- *                 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
+ * 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.
  *
- * 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.
+ * 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.
  *
- * For more info, check our website at http://www.gromacs.org
+ * 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.
  *
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
+#include "gmxpre.h"
+
 #include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gstat.h"
-#include "macros.h"
-#include "maths.h"
-#include "physics.h"
-#include "index.h"
-#include "smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/units.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "strdb.h"
-#include "xvgr.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "correl.h"
 #include "gmx_ana.h"
 #include "gromacs/fft/fft.h"
@@ -223,8 +221,11 @@ static void dump_fy(output_env_t oenv, real toler)
     DD = pow(10.0, 0.125);
     fp = xvgropen("fy.xvg", "Fig. 2, Lin2003a", "Delta", "y or fy", oenv);
     xvgr_legend(fp, asize(leg), leg, oenv);
-    fprintf(fp, "@    world 1e-05, 0, 1000, 1\n");
-    fprintf(fp, "@    xaxes scale Logarithmic\n");
+    if (output_env_get_print_xvgr_codes(oenv))
+    {
+        fprintf(fp, "@    world 1e-05, 0, 1000, 1\n");
+        fprintf(fp, "@    xaxes scale Logarithmic\n");
+    }
     for (Delta = 1e-5; (Delta <= 1000); Delta *= DD)
     {
         f = calc_fluidicity(Delta, toler);
@@ -320,7 +321,7 @@ int gmx_dos(int argc, char *argv[])
 
     npargs = asize(pa);
     ppa    = add_acf_pargs(&npargs, pa);
-    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
                            NFILE, fnm, npargs, ppa, asize(desc), desc,
                            asize(bugs), bugs, &oenv))
     {