*/
#include "gmxpre.h"
+#include "gromacs/legacyheaders/force.h"
+
#include "config.h"
#include <assert.h>
#include <math.h>
#include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/nonbonded.h"
#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/ns.h"
#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
- wallcycle_sub_start(wcycle, ewcsBONDED);
+ wallcycle_sub_start(wcycle, ewcsLISTED);
calc_gb_forces(cr, md, born, top, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
- wallcycle_sub_stop(wcycle, ewcsBONDED);
+ wallcycle_sub_stop(wcycle, ewcsLISTED);
}
#ifdef GMX_MPI
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
- /* Shift the coordinates. Must be done before bonded forces and PPPM,
+ /* Shift the coordinates. Must be done before listed forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
- * go when no bonded forces have to be evaluated.
+ * go when no listed forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
- /* Check whether we need to do bondeds or correct for exclusions */
+ /* Check whether we need to do listed interactions or correct for exclusions */
if (fr->bMolPBC &&
- ((flags & GMX_FORCE_BONDED)
+ ((flags & GMX_FORCE_LISTED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
}
debug_gmx();
- if (flags & GMX_FORCE_BONDED)
+ if (flags & GMX_FORCE_LISTED)
{
- wallcycle_sub_start(wcycle, ewcsBONDED);
+ wallcycle_sub_start(wcycle, ewcsLISTED);
calc_bonds(cr->ms,
idef, (const rvec *) x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
}
debug_gmx();
- wallcycle_sub_stop(wcycle, ewcsBONDED);
+ wallcycle_sub_stop(wcycle, ewcsLISTED);
}
where();