Merge release-5-0 into master

[alexxy/gromacs.git] / src / gromacs / mdlib / tpi.c

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 8eaa88b740e1f3fd82bbb54c96ecbd1f41723d8e..d517174f1b353d40ca35673e8fc4269e3f7e170a 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -34,28 +34,26 @@
  * 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 "config.h"
 
+#include <math.h>
+#include <stdlib.h>
 #include <string.h>
 #include <time.h>
-#include <math.h>
-#include "sysstuff.h"
+
 #include "network.h"
 #include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
-#include "main.h"
 #include "chargegroup.h"
 #include "force.h"
 #include "macros.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "typedefs.h"
 #include "update.h"
 #include "constr.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
 #include "tgroup.h"
 #include "mdebin.h"
 #include "vsite.h"
@@ -63,14 +61,15 @@
 #include "mdrun.h"
 #include "domdec.h"
 #include "gromacs/random/random.h"
-#include "physics.h"
-#include "xvgr.h"
+#include "gromacs/math/units.h"
+#include "gromacs/fileio/xvgr.h"
 #include "mdatoms.h"
 #include "ns.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
 #include "pme.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trxio.h"
@@ -381,25 +380,25 @@ double do_tpi(FILE *fplog, t_commrec *cr,
         snew(leg, 4+nener);
         e = 0;
         sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
-        leg[e++] = strdup(str);
+        leg[e++] = gmx_strdup(str);
         sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
-        leg[e++] = strdup(str);
+        leg[e++] = gmx_strdup(str);
         sprintf(str, "f. <e\\S-\\betaU\\N>");
-        leg[e++] = strdup(str);
+        leg[e++] = gmx_strdup(str);
         sprintf(str, "f. V");
-        leg[e++] = strdup(str);
+        leg[e++] = gmx_strdup(str);
         sprintf(str, "f. <Ue\\S-\\betaU\\N>");
-        leg[e++] = strdup(str);
+        leg[e++] = gmx_strdup(str);
         for (i = 0; i < ngid; i++)
         {
             sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
                     *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
-            leg[e++] = strdup(str);
+            leg[e++] = gmx_strdup(str);
         }
         if (bDispCorr)
         {
             sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
-            leg[e++] = strdup(str);
+            leg[e++] = gmx_strdup(str);
         }
         if (bCharge)
         {
@@ -407,17 +406,17 @@ double do_tpi(FILE *fplog, t_commrec *cr,
             {
                 sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
                         *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
-                leg[e++] = strdup(str);
+                leg[e++] = gmx_strdup(str);
             }
             if (bRFExcl)
             {
                 sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
-                leg[e++] = strdup(str);
+                leg[e++] = gmx_strdup(str);
             }
             if (EEL_FULL(fr->eeltype))
             {
                 sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
-                leg[e++] = strdup(str);
+                leg[e++] = gmx_strdup(str);
             }
         }
         xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);