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Renamed bonded module as 'listed-forces'
[alexxy/gromacs.git] / src / gromacs / mdlib / sim_util.c
diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index f71408148cd10583600324b841a378614a7f9998..e6686abd02d1ca3ea154f0670dafc479b2724554 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -36,70 +36,69 @@
  */
 #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,
@@ -1237,10 +1236,11 @@ void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
     }
 
     /* 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)
@@ -1320,13 +1320,13 @@ void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
         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);
     }
@@ -1335,7 +1335,7 @@ void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
     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);
 
@@ -1869,13 +1869,13 @@ void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
         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);
     }
@@ -1884,7 +1884,7 @@ void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
     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,
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