Sort all includes in src/gromacs

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

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 72a6901f9e221778df7c9781305f0ddf1b7bf3d0..7da23c74c3e055bb264fdf343c0a0bace19bf8f6 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -34,48 +34,45 @@
  * 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 <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 "txtdump.h"
-#include "typedefs.h"
-#include "update.h"
-#include "constr.h"
-#include "vec.h"
-#include "tgroup.h"
-#include "mdebin.h"
-#include "vsite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "domdec.h"
-#include "gromacs/random/random.h"
-#include "physics.h"
-#include "xvgr.h"
-#include "mdatoms.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "pme.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void global_max(t_commrec *cr, int *n)
 {
@@ -167,6 +164,11 @@ double do_tpi(FILE *fplog, t_commrec *cr,
     real bU_bin_limit      = 50;
     real bU_logV_bin_limit = bU_bin_limit + 10;
 
+    if (inputrec->cutoff_scheme == ecutsVERLET)
+    {
+        gmx_fatal(FARGS, "TPI does not work (yet) with the Verlet cut-off scheme");
+    }
+
     nnodes = cr->nnodes;
 
     top = gmx_mtop_generate_local_top(top_global, inputrec);
@@ -376,25 +378,25 @@ 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)
         {
@@ -402,17 +404,17 @@ 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);
@@ -655,7 +657,7 @@ double do_tpi(FILE *fplog, t_commrec *cr,
             bNS           = FALSE;
 
             /* Calculate long range corrections to pressure and energy */
-            calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
+            calc_dispcorr(inputrec, fr, top_global->natoms, state->box,
                           lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
             /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
             enerd->term[F_DISPCORR]  = enercorr;