* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "config.h"
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fft/fft.h"
#include "gromacs/fileio/confio.h"
-#include "copyrite.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "viewit.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
enum {
VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc,
asize(bugs), bugs, &oenv))
{
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
- read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
V = det(box);
tmass = 0;