Remove unnecessary extensions in t_filenm defaults

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

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 66825b4a3db52bb9c6f21759bbcdab7f9969bde6..42d316bb2ea8ed651c38839b21963bd0dba403b5 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -32,29 +32,31 @@
  * 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 <assert.h>
+#include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/math/units.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/statistics/statistics.h"
 #include "gmx_ana.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
+
+#include "gromacs/utility/fatalerror.h"
 
 #define SQR(x) (pow(x, 2.0))
 #define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */
 
-
 static void index_atom2mol(int *n, int *index, t_block *mols)
 {
     int nat, i, nmol, mol, j;
@@ -137,7 +139,7 @@ static gmx_bool precalc(t_topology top, real mass2[], real qmol[])
         }
     }
 
-    if (abs(qall) > 0.01)
+    if (fabs(qall) > 0.01)
     {
         printf("\n\nSystem not neutral (q=%f) will not calculate translational part of the dipole moment.\n", qall);
         bNEU = FALSE;
@@ -468,7 +470,7 @@ static void dielectric(FILE *fmj, FILE *fmd, FILE *outf, FILE *fcur, FILE *mcor,
                 xshfr[i] = 0.0;
             }
         }
-
+        assert(time != NULL);
 
 
         if (nfr == 0)
@@ -724,7 +726,7 @@ static void dielectric(FILE *fmj, FILE *fmd, FILE *outf, FILE *fcur, FILE *mcor,
 
 
 
-    if (bACF)
+    if (bACF && (ii < nvfr))
     {
         fprintf(stderr, "Integral and integrated fit to the current acf yields at t=%f:\n", time[vfr[ii]]);
         fprintf(stderr, "sigma=%8.3f (pure integral: %.3f)\n", sgk-malt*pow(time[vfr[ii]], sigma), sgk);
@@ -759,7 +761,7 @@ static void dielectric(FILE *fmj, FILE *fmd, FILE *outf, FILE *fcur, FILE *mcor,
     }
     else
     {
-        fprintf(stderr, "Too less points for a fit.\n");
+        fprintf(stderr, "Too few points for a fit.\n");
     }
 
 
@@ -856,12 +858,12 @@ int gmx_current(int argc, char *argv[])
         { efTPS,  NULL,  NULL, ffREAD }, /* this is for the topology */
         { efNDX, NULL, NULL, ffOPTRD },
         { efTRX, "-f", NULL, ffREAD },   /* and this for the trajectory */
-        { efXVG, "-o", "current.xvg", ffWRITE },
-        { efXVG, "-caf", "caf.xvg", ffOPTWR },
-        { efXVG, "-dsp", "dsp.xvg", ffWRITE },
-        { efXVG, "-md", "md.xvg", ffWRITE },
-        { efXVG, "-mj", "mj.xvg", ffWRITE},
-        { efXVG, "-mc", "mc.xvg", ffOPTWR }
+        { efXVG, "-o",   "current", ffWRITE },
+        { efXVG, "-caf", "caf",     ffOPTWR },
+        { efXVG, "-dsp", "dsp",     ffWRITE },
+        { efXVG, "-md",  "md",      ffWRITE },
+        { efXVG, "-mj",  "mj",      ffWRITE },
+        { efXVG, "-mc",  "mc",      ffOPTWR }
     };
 
 #define NFILE asize(fnm)
@@ -991,16 +993,16 @@ int gmx_current(int argc, char *argv[])
                temp, trust, bfit, efit, bvit, evit, status, isize, nmols, nshift,
                index0, indexm, mass2, qmol, eps_rf, oenv);
 
-    ffclose(fmj);
-    ffclose(fmd);
-    ffclose(fmjdsp);
+    gmx_ffclose(fmj);
+    gmx_ffclose(fmd);
+    gmx_ffclose(fmjdsp);
     if (bACF)
     {
-        ffclose(outf);
+        gmx_ffclose(outf);
     }
     if (bINT)
     {
-        ffclose(mcor);
+        gmx_ffclose(mcor);
     }
 
     return 0;