/*
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*
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
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- * 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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-
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+ * 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
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include <ctype.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "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 "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "tpxio.h"
-#include "confio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/viewit.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 "gromacs/fileio/confio.h"
#include "cmat.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/****************************************************************************/
/* This program calculates the order parameter per atom for an interface or */
/* P.J. van Maaren, November 2005 Added tetrahedral stuff */
/****************************************************************************/
-static void find_nearest_neighbours(t_topology top, int ePBC,
+static void find_nearest_neighbours(int ePBC,
int natoms, matrix box,
rvec x[], int maxidx, atom_id index[],
- real time,
real *sgmean, real *skmean,
int nslice, int slice_dim,
real sgslice[], real skslice[],
oenv);
/* loop over frames */
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
nframes = 0;
do
{
- find_nearest_neighbours(top, ePBC, natoms, box, x, isize[0], index[0], t,
+ find_nearest_neighbours(ePBC, natoms, box, x, isize[0], index[0],
&sg, &sk, nslice, slice_dim, sg_slice, sk_slice, gpbc);
for (i = 0; (i < nslice); i++)
{
fprintf(fpsk, "%f %f\n", t, sk);
nframes++;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
gmx_rmpbc_done(gpbc);
sfree(index);
sfree(isize);
- ffclose(fpsg);
- ffclose(fpsk);
+ gmx_ffclose(fpsg);
+ gmx_ffclose(fpsk);
fpsg = xvgropen(sgslfn,
"S\\sg\\N Angle Order Parameter / Slab", "(nm)", "S\\sg\\N",
fprintf(fpsk, "%10g %10g\n", (i+0.5)*box[slice_dim][slice_dim]/nslice,
sk_slice_tot[i]/nframes);
}
- ffclose(fpsg);
- ffclose(fpsk);
+ gmx_ffclose(fpsg);
+ gmx_ffclose(fpsk);
}
fprintf(stderr, "Using following groups: \n");
for (i = 0; i < ngrps; i++)
{
- fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
+ fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
}
fprintf(stderr, "\n");
teller = 0;
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
/*********** Start processing trajectory ***********/
do
{
nr_frames++;
}
- while (read_next_x(oenv, status, &t, natoms, x0, box));
+ while (read_next_x(oenv, status, &t, x0, box));
/*********** done with status file **********/
fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
0.333 * order[atom][YY]));
}
- ffclose(ord);
- ffclose(slOrd);
+ gmx_ffclose(ord);
+ gmx_ffclose(slOrd);
}
}
int gmx_order(int argc, char *argv[])
{
const char *desc[] = {
- "Compute the order parameter per atom for carbon tails. For atom i the",
+ "[THISMODULE] computes the order parameter per atom for carbon tails. For atom i the",
"vector i-1, i+1 is used together with an axis. ",
"The index file should contain only the groups to be used for calculations,",
"with each group of equivalent carbons along the relevant acyl chain in its own",
"group. There should not be any generic groups (like System, Protein) in the index",
"file to avoid confusing the program (this is not relevant to tetrahedral order",
"parameters however, which only work for water anyway).[PAR]",
- "The program can also give all",
+ "[THISMODULE] can also give all",
"diagonal elements of the order tensor and even calculate the deuterium",
"order parameter Scd (default). If the option [TT]-szonly[tt] is given, only one",
"order tensor component (specified by the [TT]-d[tt] option) is given and the",
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
{ efNDX, "-nr", NULL, ffREAD }, /* index for radial axis calculation */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
{ efXVG, "-od", "deuter", ffWRITE }, /* xvgr output file */
{ efPDB, "-ob", NULL, ffWRITE }, /* write Scd as B factors to PDB if permolecule */
const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
output_env_t oenv;
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (nslices < 1)
{
gmx_fatal(FARGS, "Can not have nslices < 1");
sgfnm = opt2fn_null("-Sg", NFILE, fnm);
skfnm = opt2fn_null("-Sk", NFILE, fnm);
ndxfnm = opt2fn_null("-n", NFILE, fnm);
- tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+ tpsfnm = ftp2fn(efTPR, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
fprintf(stderr, "Taking carbons as unsaturated!\n");
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
block = init_index(ftp2fn(efNDX, NFILE, fnm), &grpname);
index = block->index; /* get indices from t_block block */
do_view(oenv, opt2fn("-od", NFILE, fnm), NULL); /* view xvgr file */
}
- thanx(stderr);
if (distvals != NULL)
{
for (i = 0; i < nslices; ++i)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff