Renamed bonded module as 'listed-forces'

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / x2top.c

diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index 5a0c27af1bdc6eb6d0497fca0af31fa134a230d3..b7b3f7235f4aba0dca9ebfbfbee9934190d3030b 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -34,40 +34,35 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "x2top.h"
+#include "gmxpre.h"
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "x2top.h"
 
 #include <assert.h>
 
-#include "copyrite.h"
-#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "bondf.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/nm2type.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
-#include "physics.h"
-#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "gromacs/math/3dview.h"
-#include "txtdump.h"
-#include "readinp.h"
-#include "names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gen_ad.h"
-#include "gpp_nextnb.h"
-#include "vec.h"
-#include "atomprop.h"
-#include "hackblock.h"
-#include "nm2type.h"
-
-#include "gmx_fatal.h"
 
 char atp[7] = "HCNOSX";
 #define NATP (asize(atp)-1)
@@ -542,7 +537,7 @@ int gmx_x2top(int argc, char *argv[])
     bOPLS = (strcmp(forcefield, "oplsaa") == 0);
 
 
-    mymol.name = strdup(molnm);
+    mymol.name = gmx_strdup(molnm);
     mymol.nr   = 1;
 
     /* Init parameter lists */
@@ -635,10 +630,10 @@ int gmx_x2top(int argc, char *argv[])
         dump_hybridization(debug, atoms, nbonds);
     }
     close_symtab(&symtab);
-    free(mymol.name);
+    sfree(mymol.name);
 
     printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
-           ShortProgram());
+           output_env_get_program_display_name(oenv));
     printf("         Please verify atomtypes and charges by comparison to other\n");
     printf("         topologies.\n");