Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index ed2be1ace0b3a8c2d30ed9142bdc1889da61e898..eb727c8fa2ef8ac41d81311b0f3b5162fbc83884 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
@@ -34,36 +34,28 @@
  * 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 <math.h>
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "mtop_util.h"
-#include "physics.h"
-#include "main.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/eigensolver.h"
-#include "gromacs/linearalgebra/mtxio.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static double cv_corr(double nu, double T)
 {
@@ -351,7 +343,7 @@ int gmx_nmeig(int argc, char *argv[])
 
     t_filenm               fnm[] = {
         { efMTX, "-f", "hessian",    ffREAD  },
-        { efTPX, NULL, NULL,         ffREAD  },
+        { efTPR, NULL, NULL,         ffREAD  },
         { efXVG, "-of", "eigenfreq", ffWRITE },
         { efXVG, "-ol", "eigenval",  ffWRITE },
         { efXVG, "-os", "spectrum",  ffOPTWR },
@@ -360,17 +352,17 @@ int gmx_nmeig(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, 0,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
     }
 
     /* Read tpr file for volume and number of harmonic terms */
-    read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
+    read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &tpx, TRUE, &version, &generation);
     snew(top_x, tpx.natoms);
 
-    read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
+    read_tpx(ftp2fn(efTPR, NFILE, fnm), NULL, box, &natoms,
              top_x, NULL, NULL, &mtop);
     if (bCons)
     {
@@ -496,7 +488,7 @@ int gmx_nmeig(int argc, char *argv[])
     {
         fprintf (out, "%6d %15g\n", begin+i, eigenvalues[i]);
     }
-    ffclose(out);
+    gmx_ffclose(out);
 
 
     if (opt2bSet("-qc", NFILE, fnm))
@@ -585,14 +577,14 @@ int gmx_nmeig(int argc, char *argv[])
             qutot  += qu;
         }
     }
-    ffclose(out);
+    gmx_ffclose(out);
     if (NULL != spec)
     {
         for (j = 0; (j < maxspec); j++)
         {
             fprintf(spec, "%10g  %10g\n", 1.0*j, spectrum[j]);
         }
-        ffclose(spec);
+        gmx_ffclose(spec);
     }
     if (NULL != qc)
     {
@@ -602,7 +594,7 @@ int gmx_nmeig(int argc, char *argv[])
                nharm, nvsite);
         printf("Total correction to cV = %g J/mol K\n", qcvtot);
         printf("Total correction to  H = %g kJ/mol\n", qutot);
-        ffclose(qc);
+        gmx_ffclose(qc);
         please_cite(stdout, "Caleman2011b");
     }
     /* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors