Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / gen_vsite.c

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index c797392be358bd091759ab64a76197bb67443569..4d0e990044c17b47b9faf3c0d269383e98ceef72 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -34,30 +34,29 @@
  * 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 "gen_vsite.h"
 
 #include <math.h>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gen_vsite.h"
-#include "gromacs/utility/smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "vec.h"
-#include "toputil.h"
-#include "physics.h"
-#include "index.h"
-#include "names.h"
-#include "gromacs/fileio/futil.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-#include "macros.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define MAXNAME 32
 #define OPENDIR     '[' /* starting sign for directive         */
@@ -509,7 +508,7 @@ static void print_bonds(FILE *fp, int o2n[],
 }
 
 static int get_atype(int atom, t_atoms *at, int nrtp, t_restp rtp[],
-                     gmx_residuetype_t rt)
+                     gmx_residuetype_t *rt)
 {
     int      type;
     gmx_bool bNterm;
@@ -547,7 +546,7 @@ static int vsite_nm2type(const char *name, gpp_atomtype_t atype)
 }
 
 static real get_amass(int atom, t_atoms *at, int nrtp, t_restp rtp[],
-                      gmx_residuetype_t rt)
+                      gmx_residuetype_t *rt)
 {
     real     mass;
     gmx_bool bNterm;
@@ -1571,7 +1570,7 @@ void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
     char            **db;
     int               nvsiteconf, nvsitetop, cmplength;
     gmx_bool          isN, planarN, bFound;
-    gmx_residuetype_t rt;
+    gmx_residuetype_t*rt;
 
     t_vsiteconf      *vsiteconflist;
     /* pointer to a list of CH3/NH3/NH2 configuration entries.
@@ -2155,7 +2154,7 @@ void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
                 {
                     if (debug)
                     {
-                        fprintf(debug, " [%u -> %u]", params->param[i].a[j],
+                        fprintf(debug, " [%d -> %d]", params->param[i].a[j],
                                 params->param[i].a[j]-add_shift);
                     }
                     params->param[i].a[j] = params->param[i].a[j]-add_shift;
@@ -2164,7 +2163,7 @@ void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
                 {
                     if (debug)
                     {
-                        fprintf(debug, " [%u -> %d]", params->param[i].a[j],
+                        fprintf(debug, " [%d -> %d]", params->param[i].a[j],
                                 o2n[params->param[i].a[j]]);
                     }
                     params->param[i].a[j] = o2n[params->param[i].a[j]];