*
* 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 "config.h"
-#include <sysstuff.h>
-#include <string.h>
-#include <smalloc.h>
#include <ctype.h>
-#include <typedefs.h>
-#include <smalloc.h>
-#include "gromacs/fileio/tpxio.h"
-#include <macros.h>
-#include <maths.h>
-#include <atomprop.h>
-#include <names.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h> // for usleep()
+#endif
+
#include "manager.h"
-#include "gromacs/fileio/futil.h"
-#include "pbc.h"
+
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "3dview.h"
#include "nmol.h"
-#include "copyrite.h"
-#include "gstat.h"
-#include "vec.h"
-#include "statutil.h"
-#include "string2.h"
static void add_object(t_manager *man, eObject eO, atom_id ai, atom_id aj)
{
man->natom =
read_first_x(man->oenv, &man->status, trajectory, &(man->time), &(man->x),
man->box);
- man->trajfile = strdup(trajectory);
+ man->trajfile = gmx_strdup(trajectory);
if (man->natom > man->top.atoms.nr)
{
gmx_fatal(FARGS, "Topology %s (%d atoms) and trajectory %s (%d atoms) "
cool_quote(quote, 255, NULL);
sprintf(buf, "%s: %s", *man->top.name, quote);
- man->title.text = strdup(buf);
+ man->title.text = gmx_strdup(buf);
man->view = init_view(man->box);
at = &(man->top.atoms);
aps = gmx_atomprop_init();