Merge release-5-0 into master

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

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 763b6d8e5da1001ebcde6dc9a9b4af91f2971788..b86bbef806e7f0a6317fe8900035573c4612b2d3 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -34,36 +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.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
 #include <ctype.h>
-#include <stdlib.h>
 #include <limits.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
-#include "readinp.h"
-#include "warninp.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/warninp.h"
 #include "readir.h"
 #include "toputil.h"
-#include "index.h"
-#include "network.h"
-#include "vec.h"
-#include "pbc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "inputrec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/inputrec.h"
 #include "calc_verletbuf.h"
 
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
 #define MAXPTR 254
 #define NOGID  255
 
@@ -1426,7 +1425,7 @@ int str_nelem(const char *str, int maxptr, char *ptr[])
     int   np = 0;
     char *copy0, *copy;
 
-    copy0 = strdup(str);
+    copy0 = gmx_strdup(str);
     copy  = copy0;
     ltrim(copy);
     while (*copy != '\0')
@@ -1681,7 +1680,7 @@ static void do_wall_params(t_inputrec *ir,
         }
         for (i = 0; i < ir->nwall; i++)
         {
-            opts->wall_atomtype[i] = strdup(names[i]);
+            opts->wall_atomtype[i] = gmx_strdup(names[i]);
         }
 
         if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
@@ -2344,7 +2343,7 @@ void get_ir(const char *mdparin, const char *mdparout,
     {
         if (ir->efep != efepNO)
         {
-            opts->couple_moltype = strdup(is->couple_moltype);
+            opts->couple_moltype = gmx_strdup(is->couple_moltype);
             if (opts->couple_lam0 == opts->couple_lam1)
             {
                 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
@@ -2936,7 +2935,7 @@ static void decode_cos(char *s, t_cosines *cosine)
     double  a, phi;
     int     i;
 
-    t = strdup(s);
+    t = gmx_strdup(s);
     trim(t);
 
     cosine->n   = 0;
@@ -3117,7 +3116,7 @@ static void make_swap_groups(
 
 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
 {
-    int      ig = -1, i;
+    int      ig, i;
 
 
     ig            = search_string(IMDgname, grps->nr, gnames);