*
* 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 "gmxpre.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "index.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, gmx_bool bPBC)
const char *desc[] = {
"[THISMODULE] analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
- "reference positions to the first atom of each solvent molecule:[PAR]",
- "[GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
- "molecule to the midpoint between atoms 2 and 3.[BR]",
- "[GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
- "same three atoms, or, when the option [TT]-v23[tt] is set, ",
- "the angle with the vector between atoms 2 and 3.[PAR]",
+ "reference positions to the first atom of each solvent molecule:",
+ "",
+ " * [GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
+ " molecule to the midpoint between atoms 2 and 3.",
+ " * [GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
+ " same three atoms, or, when the option [TT]-v23[tt] is set, ",
+ " the angle with the vector between atoms 2 and 3.",
+ "",
"The reference can be a set of atoms or",
"the center of mass of a set of atoms. The group of solvent atoms should",
"consist of 3 atoms per solvent molecule.",
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "sori.xvg", ffWRITE },
- { efXVG, "-no", "snor.xvg", ffWRITE },
- { efXVG, "-ro", "sord.xvg", ffWRITE },
- { efXVG, "-co", "scum.xvg", ffWRITE },
- { efXVG, "-rc", "scount.xvg", ffWRITE }
+ { efXVG, NULL, "sori", ffWRITE },
+ { efXVG, "-no", "snor", ffWRITE },
+ { efXVG, "-ro", "sord", ffWRITE },
+ { efXVG, "-co", "scum", ffWRITE },
+ { efXVG, "-rc", "scount", ffWRITE }
};
#define NFILE asize(fnm)
- 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, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth-1, 2*normfac*hist1[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent normal orientation between %g and %g nm", rmin, rmax);
fp = xvgropen(opt2fn("-no", NFILE, fnm), str, "cos(\\8q\\4\\s2\\N)", "", oenv);
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth, normfac*hist2[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent orientation");
histn[i] ? histi1[i]/histn[i] : 0,
histn[i] ? histi2[i]/histn[i] : 0);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Cumulative solvent orientation");
fp = xvgropen(opt2fn("-co", NFILE, fnm), str, "r (nm)", "", oenv);
c2 += histi2[i]*normfac;
fprintf(fp, "%g %g %g\n", (i+1)*rbinw, c1, c2);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent distribution");
fp = xvgropen(opt2fn("-rc", NFILE, fnm), str, "r (nm)", "molecules/nm", oenv);
{
fprintf(fp, "%g %g\n", (i+0.5)*rbinw, histn[i]*normfac);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-no", NFILE, fnm), NULL);