*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* 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 <string.h>
-#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/utility/futil.h"
#include "gstat.h"
-#include "txtdump.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "eigio.h"
-#include "mtop_util.h"
-#include "physics.h"
-#include "main.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/math/units.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/linearalgebra/eigensolver.h"
-#include "gromacs/linearalgebra/mtxio.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
static double cv_corr(double nu, double T)
{
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
fprintf (out, "%6d %15g\n", begin+i, eigenvalues[i]);
}
- ffclose(out);
+ gmx_ffclose(out);
if (opt2bSet("-qc", NFILE, fnm))
qutot += qu;
}
}
- ffclose(out);
+ gmx_ffclose(out);
if (NULL != spec)
{
for (j = 0; (j < maxspec); j++)
{
fprintf(spec, "%10g %10g\n", 1.0*j, spectrum[j]);
}
- ffclose(spec);
+ gmx_ffclose(spec);
}
if (NULL != qc)
{
nharm, nvsite);
printf("Total correction to cV = %g J/mol K\n", qcvtot);
printf("Total correction to H = %g kJ/mol\n", qutot);
- ffclose(qc);
+ gmx_ffclose(qc);
please_cite(stdout, "Caleman2011b");
}
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors