Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index 0ea66458d4687a2ba79d7835da6b0d68e2faf1c4..a883f697a8c96dd993235a9ba07fba555e48b465 100644 (file)
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.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.
@@ -34,38 +34,42 @@
  * 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 "sysstuff.h"
-#include "gromacs/commandline/pargs.h"
 #include <string.h>
-#include "smalloc.h"
-#include "typedefs.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmx_ana.h"
 
 int gmx_genpr(int argc, char *argv[])
 {
     const char        *desc[] = {
-        "[THISMODULE] produces an include file for a topology containing",
+        "[THISMODULE] produces an #include file for a topology containing",
         "a list of atom numbers and three force constants for the",
-        "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction. A single isotropic force constant may",
+        "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction based on",
+        "the contents of the [TT]-f[tt] file. A single isotropic force constant may",
         "be given on the command line instead of three components.[PAR]",
-        "WARNING: position restraints only work for the one molecule at a time.",
-        "Position restraints are interactions within molecules, therefore",
-        "they should be included within the correct [TT][ moleculetype ][tt]",
-        "block in the topology. Since the atom numbers in every moleculetype",
-        "in the topology start at 1 and the numbers in the input file for",
-        "[THISMODULE] number consecutively from 1, [THISMODULE] will only",
-        "produce a useful file for the first molecule.[PAR]",
+        "WARNING: Position restraints are interactions within molecules, therefore",
+        "they must be included within the correct [TT][ moleculetype ][tt]",
+        "block in the topology. The atom indices within the",
+        "[TT][ position_restraints ][tt] block must be within the range of the",
+        "atom indices for that molecule type. Since the atom numbers in every",
+        "moleculetype in the topology start at 1 and the numbers in the input file",
+        "for [THISMODULE] number consecutively from 1, [THISMODULE] will only",
+        "produce a useful file for the first molecule. You may wish to",
+        "edit the resulting index file to remove the lines for later atoms,",
+        "or construct a suitable index group to provide",
+        "as input to [THISMODULE].[PAR]",
         "The [TT]-of[tt] option produces an index file that can be used for",
         "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
         "With the [TT]-disre[tt] option, half a matrix of distance restraints",
@@ -178,7 +182,7 @@ int gmx_genpr(int argc, char *argv[])
                 fprintf(out, "%d\n", i+1);
             }
         }
-        ffclose(out);
+        gmx_ffclose(out);
     }
     else if ((bDisre || bConstr) && x)
     {
@@ -226,12 +230,12 @@ int gmx_genpr(int argc, char *argv[])
                         hi = d+dd;
                         fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
                                 ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
-                                lo, hi, hi+1, 1.0);
+                                lo, hi, hi+disre_up2, 1.0);
                     }
                 }
             }
         }
-        ffclose(out);
+        gmx_ffclose(out);
     }
     else
     {
@@ -247,7 +251,7 @@ int gmx_genpr(int argc, char *argv[])
             fprintf(out, "%4d %4d %10g %10g %10g\n",
                     ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);
         }
-        ffclose(out);
+        gmx_ffclose(out);
     }
     if (xfn)
     {