*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* 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 <string.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <string.h>
#include <algorithm>
-#include "macros.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "bondf.h"
-#include "gromacs/utility/futil.h"
-#include "viewit.h"
-#include "txtdump.h"
-#include "gromacs/statistics/statistics.h"
-#include "gstat.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "names.h"
-#include "gromacs/math/units.h"
-#include "calcmu.h"
-#include "gromacs/fileio/enxio.h"
-#include "gmx_ana.h"
-#include "copyrite.h"
-#include "gromacs/fileio/trxio.h"
-
#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#define e2d(x) ENM2DEBYE*(x)
/* Swap x0 and x1 */
x0 = x1;
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
gmx_bool read_mu_from_enx(ener_file_t fmu, int Vol, ivec iMu, rvec mu, real *vol,
slab_dipole[i][ZZ]/nframes,
mutot);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, fn, "-autoscale xy -nxy");
}
close_trj(status);
}
- gmx_ffclose(outmtot);
- gmx_ffclose(outaver);
- gmx_ffclose(outeps);
+ xvgrclose(outmtot);
+ xvgrclose(outaver);
+ xvgrclose(outeps);
if (fnadip)
{
- gmx_ffclose(adip);
+ xvgrclose(adip);
}
if (cosaver)
{
- gmx_ffclose(caver);
+ xvgrclose(caver);
}
if (dip3d)
fprintf(outdd, "%10g %10f\n",
(i*mu_max)/ndipbin, dipole_bin[i]/(double)teller);
}
- gmx_ffclose(outdd);
+ xvgrclose(outdd);
sfree(dipole_bin);
}
if (bGkr)
{ "-rcmax", FALSE, etREAL, {&rcmax},
"Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used." },
{ "-phi", FALSE, etBOOL, {&bPhi},
- "Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the [TT].xpm[tt] file from the [TT]-cmap[tt] option. By default the cosine of the angle between the dipoles is plotted." },
+ "Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the [REF].xpm[ref] file from the [TT]-cmap[tt] option. By default the cosine of the angle between the dipoles is plotted." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of colors in the cmap output" },
{ "-ndegrees", FALSE, etINT, {&ndegrees},
t_filenm fnm[] = {
{ efEDR, "-en", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "Mtot", ffWRITE },
{ efXVG, "-eps", "epsilon", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm), NULL, box,
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
&natoms, NULL, NULL, NULL, top);
snew(gnx, ncos);