Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.

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

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index b03ae2a90844e41945a6b998564887b68f1c8b35..43a3180d678f69ba5d2cdae8a48dcc3e29d3a9d2 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -34,32 +34,33 @@
  * 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 <math.h>
-#include <ctype.h>
+#include "gmxpre.h"
 
-#include "sysstuff.h"
+#include <ctype.h>
+#include <math.h>
+#include <stdlib.h>
 #include <string.h>
+
 #include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char *atomname;
@@ -118,7 +119,7 @@ int get_electrons(t_electron **eltab, const char *fn)
             gmx_fatal(FARGS, "Invalid line in datafile at line %d\n", i+1);
         }
         (*eltab)[i].nr_el    = tempnr;
-        (*eltab)[i].atomname = strdup(tempname);
+        (*eltab)[i].atomname = gmx_strdup(tempname);
     }
     gmx_ffclose(in);
 
@@ -274,7 +275,7 @@ void calc_electron_density(const char *fn, atom_id **index, int gnx[],
                     slice = (z / (*slWidth));
                 }
                 sought.nr_el    = 0;
-                sought.atomname = strdup(*(top->atoms.atomname[index[n][i]]));
+                sought.atomname = gmx_strdup(*(top->atoms.atomname[index[n][i]]));
 
                 /* now find the number of electrons. This is not efficient. */
                 found = (t_electron *)
@@ -670,14 +671,14 @@ int gmx_density(int argc, char *argv[])
     t_filenm           fnm[] = { /* files for g_density       */
         { efTRX, "-f", NULL,  ffREAD },
         { efNDX, NULL, NULL,  ffOPTRD },
-        { efTPX, NULL, NULL,  ffREAD },
+        { efTPR, NULL, NULL,  ffREAD },
         { efDAT, "-ei", "electrons", ffOPTRD }, /* file with nr. of electrons */
         { efXVG, "-o", "density", ffWRITE },
     };
 
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
                            &oenv))
     {
@@ -692,7 +693,7 @@ int gmx_density(int argc, char *argv[])
     /* Calculate axis */
     axis = toupper(axtitle[0]) - 'X';
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
     if (dens_opt[0][0] == 'n')
     {
         for (i = 0; (i < top->atoms.nr); i++)