/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
-#include "tpxio.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
#include "gmx_ana.h"
int gmx_principal(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_principal[tt] calculates the three principal axes of inertia for a group",
- "of atoms.",
+ "[THISMODULE] calculates the three principal axes of inertia for a group",
+ "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
+ "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
+ "contains the x/y/z components of the first (major) principal axis for",
+ "each frame, and similarly for the middle and minor axes in paxis2.dat",
+ "and paxis3.dat."
};
static gmx_bool foo = FALSE;
matrix axes, box;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
+ char ** legend;
-
- t_filenm fnm[] = {
+ t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efDAT, "-a1", "axis1", ffWRITE },
- { efDAT, "-a2", "axis2", ffWRITE },
- { efDAT, "-a3", "axis3", ffWRITE },
- { efDAT, "-om", "moi", ffWRITE }
+ { efXVG, "-a1", "paxis1", ffWRITE },
+ { efXVG, "-a2", "paxis2", ffWRITE },
+ { efXVG, "-a3", "paxis3", ffWRITE },
+ { efXVG, "-om", "moi", ffWRITE }
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
- axis1 = ffopen(opt2fn("-a1", NFILE, fnm), "w");
- axis2 = ffopen(opt2fn("-a2", NFILE, fnm), "w");
- axis3 = ffopen(opt2fn("-a3", NFILE, fnm), "w");
- fmoi = ffopen(opt2fn("-om", NFILE, fnm), "w");
+ snew(legend, DIM);
+ for (i = 0; i < DIM; i++)
+ {
+ snew(legend[i], STRLEN);
+ sprintf(legend[i], "%c component", 'X'+i);
+ }
+
+ axis1 = xvgropen(opt2fn("-a1", NFILE, fnm), "Principal axis 1 (major axis)",
+ output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ xvgr_legend(axis1, DIM, (const char **)legend, oenv);
+
+ axis2 = xvgropen(opt2fn("-a2", NFILE, fnm), "Principal axis 2 (middle axis)",
+ output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ xvgr_legend(axis2, DIM, (const char **)legend, oenv);
+
+ axis3 = xvgropen(opt2fn("-a3", NFILE, fnm), "Principal axis 3 (minor axis)",
+ output_env_get_xvgr_tlabel(oenv), "Component (nm)", oenv);
+ xvgr_legend(axis3, DIM, (const char **)legend, oenv);
+
+ sprintf(legend[XX], "Axis 1 (major)");
+ sprintf(legend[YY], "Axis 2 (middle)");
+ sprintf(legend[ZZ], "Axis 3 (minor)");
+
+ fmoi = xvgropen(opt2fn("-om", NFILE, fnm), "Moments of inertia around inertial axes",
+ output_env_get_xvgr_tlabel(oenv), "I (au nm\\S2\\N)", oenv);
+ xvgr_legend(fmoi, DIM, (const char **)legend, oenv);
+
+ for (i = 0; i < DIM; i++)
+ {
+ sfree(legend[i]);
+ }
+ sfree(legend);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box, TRUE);
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
do
{
calc_principal_axes(&top, x, index, gnx, axes, moi);
- fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[YY][XX], axes[ZZ][XX]);
- fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][YY], axes[YY][YY], axes[ZZ][YY]);
- fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][ZZ], axes[YY][ZZ], axes[ZZ][ZZ]);
+ fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
+ fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
+ fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
fprintf(fmoi, "%15.10f %15.10f %15.10f %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
-
close_trj(status);
- ffclose(axis1);
- ffclose(axis2);
- ffclose(axis3);
- ffclose(fmoi);
- thanx(stderr);
+ xvgrclose(axis1);
+ xvgrclose(axis2);
+ xvgrclose(axis3);
+ xvgrclose(fmoi);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff