Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_energy.c

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index a0ddbfb1604f94754fa26a136a04df21a0f43fa2..3319c96e81e0a98a7c0dcc89e7ef2c5d6a58d5eb 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -34,33 +34,31 @@
  * 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 "typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
-#include "names.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "viewit.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-#include "mdebin.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static real       minthird = -1.0/3.0, minsixth = -1.0/6.0;
 
@@ -108,7 +106,7 @@ static int *select_it(int nre, char *nm[], int *nset)
     int      *set;
     gmx_bool  bVerbose = TRUE;
 
-    if ((getenv("VERBOSE")) != NULL)
+    if ((getenv("GMX_ENER_VERBOSE")) != NULL)
     {
         bVerbose = FALSE;
     }
@@ -178,7 +176,7 @@ static int *select_by_name(int nre, gmx_enxnm_t *nm, int *nset)
     const char *fm2   = "%3d  %-34s";
     char      **newnm = NULL;
 
-    if ((getenv("VERBOSE")) != NULL)
+    if ((getenv("GMX_ENER_VERBOSE")) != NULL)
     {
         bVerbose = FALSE;
     }
@@ -193,7 +191,7 @@ static int *select_by_name(int nre, gmx_enxnm_t *nm, int *nset)
     j = 0;
     for (k = 0; k < nre; k++)
     {
-        newnm[k] = strdup(nm[k].name);
+        newnm[k] = gmx_strdup(nm[k].name);
         /* Insert dashes in all the names */
         while ((ptr = strchr(newnm[k], ' ')) != NULL)
         {
@@ -2029,7 +2027,7 @@ int gmx_energy(int argc, char *argv[])
     t_filenm           fnm[] = {
         { efEDR, "-f",    NULL,      ffREAD  },
         { efEDR, "-f2",   NULL,      ffOPTRD },
-        { efTPX, "-s",    NULL,      ffOPTRD },
+        { efTPR, "-s",    NULL,      ffOPTRD },
         { efXVG, "-o",    "energy",  ffWRITE },
         { efXVG, "-viol", "violaver", ffOPTWR },
         { efXVG, "-pairs", "pairs",   ffOPTWR },
@@ -2051,7 +2049,7 @@ int gmx_energy(int argc, char *argv[])
     npargs = asize(pa);
     ppa    = add_acf_pargs(&npargs, pa);
     if (!parse_common_args(&argc, argv,
-                           PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
+                           PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -2146,7 +2144,7 @@ int gmx_energy(int argc, char *argv[])
         }
         if (bSum)
         {
-            leg[nset] = strdup("Sum");
+            leg[nset] = gmx_strdup("Sum");
             xvgr_legend(out, nset+1, (const char**)leg, oenv);
         }
         else
@@ -2174,7 +2172,7 @@ int gmx_energy(int argc, char *argv[])
 
         if (bORIRE || bOTEN)
         {
-            get_orires_parms(ftp2fn(efTPX, NFILE, fnm), &nor, &nex, &or_label, &oobs);
+            get_orires_parms(ftp2fn(efTPR, NFILE, fnm), &nor, &nex, &or_label, &oobs);
         }
 
         if (bORIRE)
@@ -2254,7 +2252,7 @@ int gmx_energy(int argc, char *argv[])
                 {
                     fort = xvgropen(opt2fn("-ort", NFILE, fnm), "Calculated orientations",
                                     "Time (ps)", "", oenv);
-                    if (bOrinst)
+                    if (bOrinst && output_env_get_print_xvgr_codes(oenv))
                     {
                         fprintf(fort, "%s", orinst_sub);
                     }
@@ -2265,7 +2263,7 @@ int gmx_energy(int argc, char *argv[])
                     fodt = xvgropen(opt2fn("-odt", NFILE, fnm),
                                     "Orientation restraint deviation",
                                     "Time (ps)", "", oenv);
-                    if (bOrinst)
+                    if (bOrinst && output_env_get_print_xvgr_codes(oenv))
                     {
                         fprintf(fodt, "%s", orinst_sub);
                     }
@@ -2283,14 +2281,14 @@ int gmx_energy(int argc, char *argv[])
                 for (j = 0; j < 3; j++)
                 {
                     sprintf(buf, "eig%d", j+1);
-                    otenleg[(bOvec ? 12 : 3)*i+j] = strdup(buf);
+                    otenleg[(bOvec ? 12 : 3)*i+j] = gmx_strdup(buf);
                 }
                 if (bOvec)
                 {
                     for (j = 0; j < 9; j++)
                     {
                         sprintf(buf, "vec%d%s", j/3+1, j%3 == 0 ? "x" : (j%3 == 1 ? "y" : "z"));
-                        otenleg[12*i+3+j] = strdup(buf);
+                        otenleg[12*i+3+j] = gmx_strdup(buf);
                     }
                 }
             }
@@ -2299,7 +2297,7 @@ int gmx_energy(int argc, char *argv[])
     }
     else if (bDisRe)
     {
-        nbounds = get_bounds(ftp2fn(efTPX, NFILE, fnm), &bounds, &index, &pair, &npairs,
+        nbounds = get_bounds(ftp2fn(efTPR, NFILE, fnm), &bounds, &index, &pair, &npairs,
                              &mtop, &top, &ir);
         snew(violaver, npairs);
         out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
@@ -2318,7 +2316,7 @@ int gmx_energy(int argc, char *argv[])
     }
     else if (bDHDL)
     {
-        get_dhdl_parms(ftp2fn(efTPX, NFILE, fnm), &ir);
+        get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), &ir);
     }
 
     /* Initiate energies and set them to zero */
@@ -2731,7 +2729,7 @@ int gmx_energy(int argc, char *argv[])
         out = xvgropen(opt2fn("-ora", NFILE, fnm),
                        "Average calculated orientations",
                        "Restraint label", "", oenv);
-        if (bOrinst)
+        if (bOrinst && output_env_get_print_xvgr_codes(oenv))
         {
             fprintf(out, "%s", orinst_sub);
         }
@@ -2746,7 +2744,7 @@ int gmx_energy(int argc, char *argv[])
         out = xvgropen(opt2fn("-oda", NFILE, fnm),
                        "Average restraint deviation",
                        "Restraint label", "", oenv);
-        if (bOrinst)
+        if (bOrinst && output_env_get_print_xvgr_codes(oenv))
         {
             fprintf(out, "%s", orinst_sub);
         }
@@ -2761,7 +2759,7 @@ int gmx_energy(int argc, char *argv[])
         out = xvgropen(opt2fn("-odr", NFILE, fnm),
                        "RMS orientation restraint deviations",
                        "Restraint label", "", oenv);
-        if (bOrinst)
+        if (bOrinst && output_env_get_print_xvgr_codes(oenv))
         {
             fprintf(out, "%s", orinst_sub);
         }