* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "runnercommon.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "runnercommon.h"
#include <string.h>
#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/rmpbc.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/vec.h"
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "analysissettings-impl.h"
}
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
- output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0, 0);
+ output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = impl_->settings_.frflags();
frflags |= TRX_NEED_X;
"Trajectory (%d atoms) does not match topology (%d atoms)",
impl_->fr->natoms, top.topology()->atoms.nr)));
}
- // TODO: Check index groups if they have been initialized based on the topology.
- /*
- if (top)
- {
- for (int i = 0; i < impl_->sel->nr(); ++i)
- {
- gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
- impl_->fr->natoms);
- }
- }
- */
}
else
{