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

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_densorder.cpp

diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 16f98c0c035d9847f0415367981008f04c0803d1..5d8a8d9bb16a67e4226cdee03ce8964541d10bb2 100644 (file)
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -32,39 +32,36 @@
  * 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 <math.h>
 #include <string.h>
 
-#include "sysstuff.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/pbcutil/pbc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/math/units.h"
 #include "dens_filter.h"
 #include "binsearch.h"
 #include "powerspect.h"
 #include "gmx_ana.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/copyrite.h"
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_DOUBLE
 #define FLOOR(x) ((int) floor(x))
@@ -615,7 +612,9 @@ static void writesurftoxpms(t_interf ***surf1, t_interf ***surf2, int tblocks, i
     sfree(yticks);
 }
 
-static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks, int xbins, int ybins, char **fnms)
+static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks,
+                     int xbins, int ybins, char **fnms,
+                     const output_env_t oenv)
 {
     FILE *raw1, *raw2;
     int   i, j, n;
@@ -627,8 +626,10 @@ static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks, int xbins,
         gmx::BinaryInformationSettings settings;
         settings.generatedByHeader(true);
         settings.linePrefix("# ");
-        gmx::printBinaryInformation(raw1, gmx::getProgramContext(), settings);
-        gmx::printBinaryInformation(raw2, gmx::getProgramContext(), settings);
+        gmx::printBinaryInformation(raw1, output_env_get_program_context(oenv),
+                                    settings);
+        gmx::printBinaryInformation(raw2, output_env_get_program_context(oenv),
+                                    settings);
     }
     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
     fprintf(raw1, "# Legend: nt nx ny\n# Xbin Ybin Z t\n");
@@ -725,7 +726,7 @@ int gmx_densorder(int argc, char *argv[])
 
 
     t_filenm fnm[] = {
-        { efTPX, "-s",  NULL, ffREAD },               /* this is for the topology */
+        { efTPR, "-s",  NULL, ffREAD },               /* this is for the topology */
         { efTRX, "-f", NULL, ffREAD },                /* and this for the trajectory */
         { efNDX, "-n", NULL, ffREAD},                 /* this is to select groups */
         { efDAT, "-o", "Density4D", ffOPTWR},         /* This is for outputting the entire 4D densityfield in binary format */
@@ -750,7 +751,7 @@ int gmx_densorder(int argc, char *argv[])
     bRawOut  = opt2bSet("-or", NFILE, fnm);
     bGraph   = opt2bSet("-og", NFILE, fnm);
     bOut     = opt2bSet("-o", NFILE, fnm);
-    top      = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top      = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
     snew(grpname, 1);
     snew(index, 1);
     snew(ngx, 1);
@@ -798,7 +799,7 @@ int gmx_densorder(int argc, char *argv[])
         {
             gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
         }
-        writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles);
+        writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles, oenv);
     }