Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/cmat.c b/src/gromacs/gmxana/cmat.c
index 788d4e791d2c8b53d4b235c6d33e5a51f4f32f1a..672a2b60b22a1795f414a289ff85bb1d52770a7c 100644 (file)
--- a/src/gromacs/gmxana/cmat.c
+++ b/src/gromacs/gmxana/cmat.c
@@ -1,48 +1,49 @@
 /*
+ * 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.
  *
- * 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 "gmxpre.h"
 
 #include "cmat.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "matio.h"
-#include "futil.h"
+
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 t_mat *init_mat(int n1, gmx_bool b1D)
 {
@@ -70,19 +71,19 @@ void copy_t_mat(t_mat *dst, t_mat *src)
 
     if (dst->nn != src->nn)
     {
-        fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n",dst->nn,src->nn);
+        fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n", dst->nn, src->nn);
         return;
     }
     dst->maxrms = src->maxrms;
     dst->minrms = src->minrms;
     dst->sumrms = src->sumrms;
-    for(i = 0; (i < src->nn); i++)
+    for (i = 0; (i < src->nn); i++)
     {
-        for(j = 0; (j < src->nn); j++)
+        for (j = 0; (j < src->nn); j++)
         {
             dst->mat[i][j] = src->mat[i][j];
         }
-        dst->erow[i] = src->erow[i];
+        dst->erow[i]  = src->erow[i];
         dst->m_ind[i] = src->m_ind[i];
     }
 }
@@ -230,7 +231,7 @@ void low_rmsd_dist(const char *fn, real maxrms, int nn, real **mat,
     {
         fprintf(fp, "%10g  %10d\n", i/fac, histo[i]);
     }
-    ffclose(fp);
+    gmx_ffclose(fp);
     sfree(histo);
 }