*/
#include "gmxpre.h"
+#include "gromacs/legacyheaders/sim_util.h"
+
#include "config.h"
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/bondf.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/imd/imd.h"
#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
#include "gromacs/legacyheaders/constr.h"
#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "gromacs/legacyheaders/qmmm.h"
-
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "nbnxn_cuda/nbnxn_cuda.h"
-#include "nb_verlet.h"
+#include "adress.h"
void print_time(FILE *out,
gmx_walltime_accounting_t walltime_accounting,
}
/* We calculate the non-bonded forces, when done on the CPU, here.
- * We do this before calling do_force_lowlevel, as in there bondeds
- * forces are calculated before PME, which does communication.
- * With this order, non-bonded and bonded force calculation imbalance
- * can be balanced out by the domain decomposition load balancing.
+ * We do this before calling do_force_lowlevel, because in that
+ * function, the listed forces are calculated before PME, which
+ * does communication. With this order, non-bonded and listed
+ * force calculation imbalance can be balanced out by the domain
+ * decomposition load balancing.
*/
if (!bUseOrEmulGPU)
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
+ if ((flags & GMX_FORCE_LISTED) && top->idef.il[F_POSRES].nr > 0)
{
posres_wrapper(flags, inputrec, nrnb, top, box, x,
enerd, lambda, fr);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
+ if ((flags & GMX_FORCE_LISTED) && top->idef.il[F_FBPOSRES].nr > 0)
{
fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
}
do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
flags, &cycles_pme);
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
+ if ((flags & GMX_FORCE_LISTED) && top->idef.il[F_POSRES].nr > 0)
{
posres_wrapper(flags, inputrec, nrnb, top, box, x,
enerd, lambda, fr);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
+ if ((flags & GMX_FORCE_LISTED) && top->idef.il[F_FBPOSRES].nr > 0)
{
fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
}
do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda,
graph, &(top->excls), fr->mu_tot,
flags,
int nfile, const t_filenm fnm[],
gmx_mdoutf_t *outf, t_mdebin **mdebin,
tensor force_vir, tensor shake_vir, rvec mu_tot,
- gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags)
+ gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_wallcycle_t wcycle)
{
int i, j, n;
real tmpt, mod;
if (nfile != -1)
{
- *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv);
+ *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv, wcycle);
*mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
mtop, ir, mdoutf_get_fp_dhdl(*outf));