* 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 "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "index.h"
-#include "macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "viewit.h"
-#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void gyro_eigen(double **gyr, double *eig, double **eigv, int *ord)
{
};
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "polystat", ffWRITE },
gmx_rmpbc_t gpbc = NULL;
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
NULL, box, &natoms, NULL, NULL, NULL, top);
fprintf(stderr, "Select a group of polymer mainchain atoms:\n");
for (d2 = 0; d2 < DIM; d2++)
{
sprintf(buf, "eig%d %c", d+1, 'x'+d2);
- legp[d*DIM+d2] = strdup(buf);
+ legp[d*DIM+d2] = gmx_strdup(buf);
}
}
xvgr_legend(outv, DIM*DIM, (const char**)legp, oenv);
/* Handle printing of internal distances. */
if (outi)
{
- fprintf(outi, "@ xaxes scale Logarithmic\n");
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(outi, "@ xaxes scale Logarithmic\n");
+ }
ymax = -1;
ymin = 1e300;
j = index[molind[1]-1] - index[molind[0]]; /* Polymer length -1. */