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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pbc.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "pdbio.h"
-#include "confio.h"
-#include "tpxio.h"
-#include "matio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "txtdump.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "eigio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
#include "gmx_ana.h"
+#include "gromacs/math/do_fit.h"
+
static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
{
int i;
int g, s, i;
real min, max, xsp, ysp;
- out = ffopen(file, "w");
+ out = gmx_ffopen(file, "w");
if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
{
fprintf(out, "@ autoscale onread none\n");
{
for (i = 0; i < n; i++)
{
- if (bSplit && i > 0 && abs(x[i]) < 1e-5)
+ if (bSplit && i > 0 && fabs(x[i]) < 1e-5)
{
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(out, "&\n");
- }
+ fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(out, "%10.4f %10.5f\n",
x[i]*scale_x, y ? y[g][i] : sy[g][s][i]);
}
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(out, "&\n");
- }
+ fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
- ffclose(out);
+ gmx_ffclose(out);
}
static void
rlo.r = 1; rlo.g = 1; rlo.b = 1;
rhi.r = 0; rhi.g = 0; rhi.b = 0;
nlevels = 41;
- out = ffopen(matfile, "w");
+ out = gmx_ffopen(matfile, "w");
write_xpm(out, 0, "Eigenvector inner-products", "in.prod.", "run 1", "run 2",
nx, ny, t_x, t_y, mat, 0.0, max, rlo, rhi, &nlevels);
- ffclose(out);
+ gmx_ffclose(out);
}
static void overlap(const char *outfile, int natoms,
out = xvgropen(outfile, "Subspace overlap",
"Eigenvectors of trajectory 2", "Overlap", oenv);
- fprintf(out, "@ subtitle \"using %d eigenvectors of trajectory 1\"\n",
- noutvec);
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(out, "@ subtitle \"using %d eigenvectors of trajectory 1\"\n", noutvec);
+ }
overlap = 0;
for (x = 0; x < nvec2; x++)
{
fprintf(out, "%5d %5.3f\n", eignr2[x]+1, overlap/noutvec);
}
- ffclose(out);
+ gmx_ffclose(out);
}
static void project(const char *trajfile, t_topology *top, int ePBC, matrix topbox,
for (v = 0; v < noutvec; v++)
{
sprintf(str, "vec %d", eignr[outvec[v]]+1);
- ylabel[v] = strdup(str);
+ ylabel[v] = gmx_strdup(str);
}
sprintf(str, "projection on eigenvectors (%s)", proj_unit);
write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
oenv);
for (i = 0; i < nframes; i++)
{
- if (bSplit && i > 0 && abs(inprod[noutvec][i]) < 1e-5)
+ if (bSplit && i > 0 && fabs(inprod[noutvec][i]) < 1e-5)
{
- fprintf(xvgrout, "&\n");
+ fprintf(xvgrout, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(xvgrout, "%10.5f %10.5f\n", inprod[0][i], inprod[noutvec-1][i]);
}
- ffclose(xvgrout);
+ gmx_ffclose(xvgrout);
}
if (threedplotfile)
rvec *x;
real *b = NULL;
matrix box;
- char *resnm, *atnm, pdbform[STRLEN];
+ char *resnm, *atnm;
gmx_bool bPDB, b4D;
FILE *out;
init_t_atoms(&atoms, nframes, FALSE);
snew(x, nframes);
snew(b, nframes);
- atnm = strdup("C");
- resnm = strdup("PRJ");
+ atnm = gmx_strdup("C");
+ resnm = gmx_strdup("PRJ");
if (nframes > 10000)
{
}
if ( ( b4D || bSplit ) && bPDB)
{
- strcpy(pdbform, get_pdbformat());
- strcat(pdbform, "%8.4f%8.4f\n");
-
- out = ffopen(threedplotfile, "w");
+ out = gmx_ffopen(threedplotfile, "w");
fprintf(out, "HEADER %s\n", str);
if (b4D)
{
j = 0;
for (i = 0; i < atoms.nr; i++)
{
- if (j > 0 && bSplit && abs(inprod[noutvec][i]) < 1e-5)
+ if (j > 0 && bSplit && fabs(inprod[noutvec][i]) < 1e-5)
{
fprintf(out, "TER\n");
j = 0;
}
- fprintf(out, pdbform, "ATOM", i+1, "C", "PRJ", ' ', j+1,
- PR_VEC(10*x[i]), 1.0, 10*b[i]);
+ gmx_fprintf_pdb_atomline(out, epdbATOM, i+1, "C", ' ', "PRJ", ' ', j+1, ' ',
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 10*b[i], "");
if (j > 0)
{
fprintf(out, "CONECT%5d%5d\n", i, i+1);
j++;
}
fprintf(out, "TER\n");
- ffclose(out);
+ gmx_ffclose(out);
}
else
{
{
v = outvec[g];
sprintf(str, "vec %d", eignr[v]+1);
- ylabel[g] = strdup(str);
+ ylabel[g] = gmx_strdup(str);
snew(y[g], 4);
for (s = 0; s < 4; s++)
{
gmx_fatal(FARGS, "Selected vector %d is larger than the number of eigenvalues (%d)", eignr[v]+1, neig);
}
sprintf(str, "vec %d", eignr[v]+1);
- ylabel[g] = strdup(str);
+ ylabel[g] = gmx_strdup(str);
snew(y[g], natoms);
for (i = 0; i < natoms; i++)
{
int gmx_anaeig(int argc, char *argv[])
{
static const char *desc[] = {
- "[TT]g_anaeig[tt] analyzes eigenvectors. The eigenvectors can be of a",
- "covariance matrix ([TT]g_covar[tt]) or of a Normal Modes analysis",
- "([TT]g_nmeig[tt]).[PAR]",
+ "[THISMODULE] analyzes eigenvectors. The eigenvectors can be of a",
+ "covariance matrix ([gmx-covar]) or of a Normal Modes analysis",
+ "([gmx-nmeig]).[PAR]",
"When a trajectory is projected on eigenvectors, all structures are",
"fitted to the structure in the eigenvector file, if present, otherwise",
"since the pc's of random diffusion are cosines with the number",
"of periods equal to half the pc index.",
"The cosine content of the pc's can be calculated with the program",
- "[TT]g_analyze[tt].[PAR]",
+ "[gmx-analyze].[PAR]",
"[TT]-2d[tt]: calculate a 2d projection of a trajectory on eigenvectors",
"[TT]-first[tt] and [TT]-last[tt].[PAR]",
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
snew(xrefp, atoms->nr);
if (xref1 != NULL)
{
+ /* Safety check between selected fit-group and reference structure read from the eigenvector file */
+ if (natoms != nfit)
+ {
+ gmx_fatal(FARGS, "you selected a group with %d elements instead of %d, your selection does not fit the reference structure in the eigenvector file.", nfit, natoms);
+ }
for (i = 0; (i < nfit); i++)
{
copy_rvec(xref1[i], xrefp[ifit[i]]);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff