/*
+ * 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.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Green Red Orange Magenta Azure Cyan Skyblue
+ * 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 <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 "gromacs/fileio/futil.h"
-#include "statutil.h"
-#include "index.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 "mshift.h"
-#include "xvgr.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "txtdump.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++)
{
#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