Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index 575c1ead06648241a3b3e30ef34fadf01ba26bd7..7c1ec8411c9443f5838ec253b7836984c13d02d6 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -36,37 +36,28 @@
  * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
  * probably also holds copyright to the following code.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
 #include <math.h>
 #include <stdlib.h>
 #include <ctype.h>
 #include <string.h>
-#include "readinp.h"
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "statutil.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/matio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "txtdump.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "eigio.h"
-#include "index.h"
-#include "string2.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 
 typedef struct
 {
@@ -624,7 +615,7 @@ int gmx_make_edi(int argc, char *argv[])
         "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
         "is not very parallel-friendly from an implementation point of view. Because",
         "parallel ED requires some extra communication, expect the performance to be",
-        "lower as in a free MD simulation, especially on a large number of nodes and/or",
+        "lower as in a free MD simulation, especially on a large number of ranks and/or",
         "when the ED group contains a lot of atoms. [PAR]",
         "Please also note that if your ED group contains more than a single protein,",
         "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
@@ -679,7 +670,7 @@ int gmx_make_edi(int argc, char *argv[])
     static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
     static const char* ConstForceStr;
     static real      * evStepList[evStepNr];
-    static real        radfix   = 0.0;
+    static real        radstep  = 0.0;
     static real        deltaF0  = 150;
     static real        deltaF   = 0;
     static real        tau      = .1;
@@ -715,7 +706,7 @@ int gmx_make_edi(int argc, char *argv[])
           "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
         { "-accdir", FALSE, etSTR, {&evParams[1]},
           "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
-        { "-radstep", FALSE, etREAL, {&radfix},
+        { "-radstep", FALSE, etREAL, {&radstep},
           "Stepsize (nm/step) for fixed increment radius expansion"},
         { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
           "Maximum number of steps per cycle" },
@@ -821,12 +812,12 @@ int gmx_make_edi(int argc, char *argv[])
                     }
                 }
             }
-            else if (ev_class == evRADFIX && opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
+            else if (ev_class == evRADFIX)
             {
                 snew(evStepList[ev_class], nvecs);
                 for (i = 0; i < nvecs; i++)
                 {
-                    evStepList[ev_class][i] = radfix;
+                    evStepList[ev_class][i] = radstep;
                 }
             }
             else if (ev_class == evFLOOD)
@@ -864,7 +855,6 @@ int gmx_make_edi(int argc, char *argv[])
         printf("\n");
     }
 
-    EigvecFile = NULL;
     EigvecFile = opt2fn("-f", NFILE, fnm);
 
     /*read eigenvectors from eigvec.trr*/
@@ -984,7 +974,7 @@ int gmx_make_edi(int argc, char *argv[])
     }
 
     /* Write edi-file */
-    write_the_whole_thing(ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);
+    write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);
 
     return 0;
 }