/*
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*
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdlib.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.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 "rmpbc.h"
-#include "xtcio.h"
-#include "gmx_ana.h"
-
-
-static void periodic_dist(matrix box, rvec x[], int n, atom_id index[],
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.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/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+
+static void periodic_dist(int ePBC,
+ matrix box, rvec x[], int n, atom_id index[],
real *rmin, real *rmax, int *min_ind)
{
-#define NSHIFT 26
- int sx, sy, sz, i, j, s;
+#define NSHIFT_MAX 26
+ int nsz, nshift, sx, sy, sz, i, j, s;
real sqr_box, r2min, r2max, r2;
- rvec shift[NSHIFT], d0, d;
+ rvec shift[NSHIFT_MAX], d0, d;
- sqr_box = sqr(min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ])));
+ sqr_box = min(norm2(box[XX]), norm2(box[YY]));
+ if (ePBC == epbcXYZ)
+ {
+ sqr_box = min(sqr_box, norm2(box[ZZ]));
+ nsz = 1;
+ }
+ else if (ePBC == epbcXY)
+ {
+ nsz = 0;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist",
+ epbc_names[ePBC]);
+ nsz = 0; /* Keep compilers quiet */
+ }
- s = 0;
- for (sz = -1; sz <= 1; sz++)
+ nshift = 0;
+ for (sz = -nsz; sz <= nsz; sz++)
{
for (sy = -1; sy <= 1; sy++)
{
{
for (i = 0; i < DIM; i++)
{
- shift[s][i] = sx*box[XX][i]+sy*box[YY][i]+sz*box[ZZ][i];
+ shift[nshift][i] =
+ sx*box[XX][i] + sy*box[YY][i] + sz*box[ZZ][i];
}
- s++;
+ nshift++;
}
}
}
{
r2max = r2;
}
- for (s = 0; s < NSHIFT; s++)
+ for (s = 0; s < nshift; s++)
{
rvec_add(d0, shift[s], d);
r2 = norm2(d);
if (NULL != top)
{
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
bFirst = TRUE;
gmx_rmpbc(gpbc, natoms, box, x);
}
- periodic_dist(box, x, n, index, &rmin, &rmax, ind_min);
+ periodic_dist(ePBC, box, x, n, index, &rmin, &rmax, ind_min);
if (rmin < rmint)
{
rmint = rmin;
ind_mini = ind_min[0];
ind_minj = ind_min[1];
}
- if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
+ if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
{
- fprintf(out, "&\n");
+ fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
output_env_conv_time(oenv, t), rmin, rmax, norm(box[0]), norm(box[1]), norm(box[2]));
bFirst = FALSE;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
if (NULL != top)
{
gmx_rmpbc_done(gpbc);
}
- ffclose(out);
+ gmx_ffclose(out);
fprintf(stdout,
"\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : NULL;
- atm = afile ? ffopen(afile, "w") : NULL;
+ atm = afile ? gmx_ffopen(afile, "w") : NULL;
trxout = xfile ? open_trx(xfile, "w") : NULL;
if (bMat)
{
snew(leg, 1);
sprintf(buf, "Internal in %s", grpn[0]);
- leg[0] = strdup(buf);
+ leg[0] = gmx_strdup(buf);
xvgr_legend(dist, 0, (const char**)leg, oenv);
if (num)
{
for (k = i+1; (k < ng); k++, j++)
{
sprintf(buf, "%s-%s", grpn[i], grpn[k]);
- leg[j] = strdup(buf);
+ leg[j] = gmx_strdup(buf);
}
}
xvgr_legend(dist, j, (const char**)leg, oenv);
for (i = 0; (i < ng-1); i++)
{
sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
- leg[i] = strdup(buf);
+ leg[i] = gmx_strdup(buf);
}
xvgr_legend(dist, ng-1, (const char**)leg, oenv);
if (num)
bFirst = TRUE;
do
{
- if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
+ if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
{
- fprintf(dist, "&\n");
+ fprintf(dist, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
if (num)
{
- fprintf(num, "&\n");
+ fprintf(num, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
if (atm)
{
- fprintf(atm, "&\n");
+ fprintf(atm, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
fprintf(dist, "%12e", output_env_conv_time(oenv, t));
fprintf(respertime, "\n");
}
}
- while (read_next_x(oenv, status, &t, natoms, x0, box));
+ while (read_next_x(oenv, status, &t, x0, box));
close_trj(status);
- ffclose(dist);
+ gmx_ffclose(dist);
if (num)
{
- ffclose(num);
+ gmx_ffclose(num);
}
if (atm)
{
- ffclose(atm);
+ gmx_ffclose(atm);
}
if (trxout)
{
return nres;
}
-void dump_res(FILE *out, int nres, atom_id *resindex, int n, atom_id index[])
+void dump_res(FILE *out, int nres, atom_id *resindex, atom_id index[])
{
int i, j;
int gmx_mindist(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_mindist[tt] computes the distance between one group and a number of",
+ "[THISMODULE] computes the distance between one group and a number of",
"other groups. Both the minimum distance",
"(between any pair of atoms from the respective groups)",
"and the number of contacts within a given",
"each direction is considered, giving a total of 26 shifts.",
"It also plots the maximum distance within the group and the lengths",
"of the three box vectors.[PAR]",
- "Other programs that calculate distances are [TT]g_dist[tt]",
- "and [TT]g_bond[tt]."
+ "Also [gmx-distance] calculates distances."
};
const char *bugs[] = {
"The [TT]-pi[tt] option is very slow."
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | 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 | PCA_TIME_UNIT,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
trxfnm = ftp2fn(efTRX, NFILE, fnm);
ndxfnm = ftp2fn_null(efNDX, NFILE, fnm);
gnx[0], index[0], &residues);
if (debug)
{
- dump_res(debug, nres, residues, gnx[0], index[0]);
+ dump_res(debug, nres, residues, index[0]);
}
}
do_view(oenv, numfnm, "-nxy");
}
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff