Remove dependence of compute_globals on t_state

This change makes the different function related to compute_globals
request the fields of t_state explicitly, instead of simply taking
a pointer to the full t_state object. This simplifies refactoring
the t_state object in future commits. This change also clarifies why
both state->box and an additional parameter `matrix box` is required -
the latter one is the box at the last complete timestep in do_md and
has been renamed accordingly.

Note that in the documentation to checkNumberOfBondedInteractions(),
which was changed in a similar way, the argument `state` was
described as being the global state. Throughout the code, the local
state was used, however. This part of the documentation is now
changed, but if that was intended, then a follow-up change fixing
this might be necessary.

Change-Id: If913656fe9bf07567a29f68592402bb5ff17fc52

diff --git a/src/gromacs/domdec/domdec.h b/src/gromacs/domdec/domdec.h
index 017a6679d581f5d457820a4d5375293221025c70..e216dd31ad469b224e5ed76f1100bb5f08668191 100644 (file)
--- a/src/gromacs/domdec/domdec.h
+++ b/src/gromacs/domdec/domdec.h
@@ -265,7 +265,8 @@ void dd_print_missing_interactions(const gmx::MDLogger  &mdlog,
                                    int                   local_count,
                                    const gmx_mtop_t     *top_global,
                                    const gmx_localtop_t *top_local,
-                                   const t_state        *state_local);
+                                   const rvec           *x,
+                                   const matrix          box);
 
 /*! \brief Generate and store the reverse topology */
 void dd_make_reverse_top(FILE *fplog,

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index e91353175b4c5cb2696b729ad3dff3df0f274581..72578df261400a11abe1c3dbb783cbbb411c5155 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -342,7 +342,8 @@ void dd_print_missing_interactions(const gmx::MDLogger  &mdlog,
                                    int                   local_count,
                                    const gmx_mtop_t     *top_global,
                                    const gmx_localtop_t *top_local,
-                                   const t_state        *state_local)
+                                   const rvec           *x,
+                                   const matrix          box)
 {
     int             ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
     int             ftype, nral;
@@ -408,7 +409,7 @@ void dd_print_missing_interactions(const gmx::MDLogger  &mdlog,
 
     print_missing_interactions_atoms(mdlog, cr, top_global, &top_local->idef);
     write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
-                 -1, state_local->x.rvec_array(), state_local->box);
+                 -1, x, box);
 
     std::string errorMessage;
 

diff --git a/src/gromacs/domdec/partition.cpp b/src/gromacs/domdec/partition.cpp
index 62e2a0741deb19bd97cf039552ea5a97a5bb8799..b05843ae5b42a788230b2c81e40c222a8ab47698 100644 (file)
--- a/src/gromacs/domdec/partition.cpp
+++ b/src/gromacs/domdec/partition.cpp
@@ -3351,14 +3351,15 @@ void checkNumberOfBondedInteractions(const gmx::MDLogger  &mdlog,
                                      int                   totalNumberOfBondedInteractions,
                                      const gmx_mtop_t     *top_global,
                                      const gmx_localtop_t *top_local,
-                                     const t_state        *state,
+                                     const rvec           *x,
+                                     const matrix          box,
                                      bool                 *shouldCheckNumberOfBondedInteractions)
 {
     if (*shouldCheckNumberOfBondedInteractions)
     {
         if (totalNumberOfBondedInteractions != cr->dd->nbonded_global)
         {
-            dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global, top_local, state); // Does not return
+            dd_print_missing_interactions(mdlog, cr, totalNumberOfBondedInteractions, top_global, top_local, x, box); // Does not return
         }
         *shouldCheckNumberOfBondedInteractions = false;
     }

diff --git a/src/gromacs/domdec/partition.h b/src/gromacs/domdec/partition.h
index 9f271cbcf04f5499b5506c95fb031416d5d79c6a..dbe641c7987b59f25bfaf4b8203cff7cab87e750 100644 (file)
--- a/src/gromacs/domdec/partition.h
+++ b/src/gromacs/domdec/partition.h
@@ -117,7 +117,8 @@ void dd_partition_system(FILE                    *fplog,
  * \param[in]    totalNumberOfBondedInteractions        Result of the global reduction over the number of bonds treated in each domain
  * \param[in]    top_global                             Global topology for the error message
  * \param[in]    top_local                              Local topology for the error message
- * \param[in]    state                                  Global state for the error message
+ * \param[in]    x                                      Position vector for the error message
+ * \param[in]    box                                    Box matrix for the error message
  * \param[in,out] shouldCheckNumberOfBondedInteractions Whether we should do the check. Always set to false.
  */
 void checkNumberOfBondedInteractions(const gmx::MDLogger  &mdlog,
@@ -125,7 +126,8 @@ void checkNumberOfBondedInteractions(const gmx::MDLogger  &mdlog,
                                      int                   totalNumberOfBondedInteractions,
                                      const gmx_mtop_t     *top_global,
                                      const gmx_localtop_t *top_local,
-                                     const t_state        *state,
+                                     const rvec           *x,
+                                     const matrix          box,
                                      bool                 *shouldCheckNumberOfBondedInteractions);
 
 #endif

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index 3fd69ace3cabf1cc8d52d41be06b95795384f055..d3d1614c9103117d7c1c79a37002f18ca8c24871 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -155,12 +155,12 @@ int multisim_min(const gmx_multisim_t *ms, int nmin, int n)
    e.g. bReadEkin is only true when restoring from checkpoint */
 void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
                      t_forcerec *fr, gmx_ekindata_t *ekind,
-                     t_state *state, t_mdatoms *mdatoms,
+                     rvec *x, rvec *v, matrix box, real vdwLambda, t_mdatoms *mdatoms,
                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                      gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
                      tensor pres, rvec mu_tot, gmx::Constraints *constr,
                      gmx::SimulationSignaller *signalCoordinator,
-                     matrix box, int *totalNumberOfBondedInteractions,
+                     matrix lastbox, int *totalNumberOfBondedInteractions,
                      gmx_bool *bSumEkinhOld, int flags)
 {
     gmx_bool bEner, bPres, bTemp;
@@ -202,7 +202,9 @@ void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_input
         }
         if (!bReadEkin)
         {
-            calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
+            calc_ke_part(
+                    x, v, box,
+                    &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
         }
     }
 
@@ -210,7 +212,7 @@ void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_input
     if (bStopCM)
     {
         calc_vcm_grp(0, mdatoms->homenr, mdatoms,
-                     state->x.rvec_array(), state->v.rvec_array(), vcm);
+                     x, v, vcm);
     }
 
     if (bTemp || bStopCM || bPres || bEner || bConstrain || bCheckNumberOfBondedInteractions)
@@ -251,10 +253,10 @@ void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_input
         rvec *xPtr = nullptr;
         if (vcm->mode == ecmANGULAR || (vcm->mode == ecmLINEAR_ACCELERATION_CORRECTION && !(flags & CGLO_INITIALIZATION)))
         {
-            xPtr = state->x.rvec_array();
+            xPtr = x;
         }
         do_stopcm_grp(*mdatoms,
-                      xPtr, state->v.rvec_array(), *vcm);
+                      xPtr, v, *vcm);
         inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
     }
 
@@ -290,7 +292,7 @@ void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_input
          * Use the box from last timestep since we already called update().
          */
 
-        enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);
+        enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, lastbox, ekind->ekin, total_vir, pres);
     }
 
     /* ##########  Long range energy information ###### */
@@ -302,7 +304,7 @@ void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_input
            total_vir and pres tensors */
 
         const DispersionCorrection::Correction correction =
-            fr->dispersionCorrection->calculate(box, state->lambda[efptVDW]);
+            fr->dispersionCorrection->calculate(lastbox, vdwLambda);
 
         if (bEner)
         {

diff --git a/src/gromacs/mdlib/md_support.h b/src/gromacs/mdlib/md_support.h
index 87029dcd3cebe131b732e4e33849c8688f8a52ba..6a2ca1d059905521f7ba67fd5079a6d1b92b4c57 100644 (file)
--- a/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -124,12 +124,12 @@ int multisim_min(const gmx_multisim_t *ms, int nmin, int n);
 
 void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
                      t_forcerec *fr, gmx_ekindata_t *ekind,
-                     t_state *state, t_mdatoms *mdatoms,
+                     rvec *x, rvec *v, matrix box, real vdwLambda, t_mdatoms *mdatoms,
                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                      gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
                      tensor pres, rvec mu_tot, gmx::Constraints *constr,
                      gmx::SimulationSignaller *signalCoordinator,
-                     matrix box, int *totalNumberOfBondedInteractions,
+                     matrix lastbox, int *totalNumberOfBondedInteractions,
                      gmx_bool *bSumEkinhOld, int flags);
 /* Compute global variables during integration */
 

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index 81b0877eeb1c905915861488a33ad13df3ab2633..4b121d1bcff273f7aa262cf06d06de94c8c1ad50 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -1218,16 +1218,18 @@ static void calc_ke_part_visc(const matrix box, const rvec x[], const rvec v[],
     inc_nrnb(nrnb, eNR_EKIN, homenr);
 }
 
-void calc_ke_part(const t_state *state, const t_grpopts *opts, const t_mdatoms *md,
-                  gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
+void calc_ke_part(
+        rvec *x, rvec *v, matrix box,
+        const t_grpopts *opts, const t_mdatoms *md,
+        gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
 {
     if (ekind->cosacc.cos_accel == 0)
     {
-        calc_ke_part_normal(state->v.rvec_array(), opts, md, ekind, nrnb, bEkinAveVel);
+        calc_ke_part_normal(v, opts, md, ekind, nrnb, bEkinAveVel);
     }
     else
     {
-        calc_ke_part_visc(state->box, state->x.rvec_array(), state->v.rvec_array(), opts, md, ekind, nrnb, bEkinAveVel);
+        calc_ke_part_visc(box, x, v, opts, md, ekind, nrnb, bEkinAveVel);
     }
 }
 

diff --git a/src/gromacs/mdlib/update.h b/src/gromacs/mdlib/update.h
index 6b1f3ad6c475282f9342ac90e9e6c644132930cb..ffc75a45c3c4376bef06b03035cb83e244058199 100644 (file)
--- a/src/gromacs/mdlib/update.h
+++ b/src/gromacs/mdlib/update.h
@@ -200,8 +200,10 @@ void finish_update(const t_inputrec       *inputrec,
 
 /* Return TRUE if OK, FALSE in case of Shake Error */
 
-void calc_ke_part(const t_state *state, const t_grpopts *opts, const t_mdatoms *md,
-                  gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
+void calc_ke_part(
+        rvec *x, rvec *v, matrix box,
+        const t_grpopts *opts, const t_mdatoms *md,
+        gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
 /*
  * Compute the partial kinetic energy for home particles;
  * will be accumulated in the calling routine.

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 77d2dc5cb4188837a1d512e375d3e2ebbee6368f..4a210e5b151ba0c479a88260f6d3576ab7ce0177 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -539,14 +539,16 @@ void gmx::Simulator::do_md()
             cglo_flags_iteration |= CGLO_STOPCM;
             cglo_flags_iteration &= ~CGLO_TEMPERATURE;
         }
-        compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+        compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                        state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                        mdatoms, nrnb, &vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags_iteration
                         | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
     }
     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                    top_global, &top, state,
+                                    top_global, &top, state->x.rvec_array(), state->box,
                                     &shouldCheckNumberOfBondedInteractions);
     if (ir->eI == eiVVAK)
     {
@@ -556,7 +558,9 @@ void gmx::Simulator::do_md()
            kinetic energy calculation.  This minimized excess variables, but
            perhaps loses some logic?*/
 
-        compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+        compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                        state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                        mdatoms, nrnb, &vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         nullptr, &bSumEkinhOld,
@@ -831,13 +835,15 @@ void gmx::Simulator::do_md()
             /* We need the kinetic energy at minus the half step for determining
              * the full step kinetic energy and possibly for T-coupling.*/
             /* This may not be quite working correctly yet . . . . */
-            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+            compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                            state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                            mdatoms, nrnb, &vcm,
                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
                             constr, &nullSignaller, state->box,
                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
                             CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                            top_global, &top, state,
+                                            top_global, &top, state->x.rvec_array(), state->box,
                                             &shouldCheckNumberOfBondedInteractions);
         }
         clear_mat(force_vir);
@@ -986,7 +992,9 @@ void gmx::Simulator::do_md()
             if (bGStat || do_per_step(step-1, nstglobalcomm))
             {
                 wallcycle_stop(wcycle, ewcUPDATE);
-                compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+                compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                                state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                                mdatoms, nrnb, &vcm,
                                 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                                 constr, &nullSignaller, state->box,
                                 &totalNumberOfBondedInteractions, &bSumEkinhOld,
@@ -1007,7 +1015,7 @@ void gmx::Simulator::do_md()
                    b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
                    EkinAveVel because it's needed for the pressure */
                 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                                top_global, &top, state,
+                                                top_global, &top, state->x.rvec_array(), state->box,
                                                 &shouldCheckNumberOfBondedInteractions);
                 wallcycle_start(wcycle, ewcUPDATE);
             }
@@ -1041,7 +1049,9 @@ void gmx::Simulator::do_md()
                     /* We need the kinetic energy at minus the half step for determining
                      * the full step kinetic energy and possibly for T-coupling.*/
                     /* This may not be quite working correctly yet . . . . */
-                    compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+                    compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                                    state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                                    mdatoms, nrnb, &vcm,
                                     wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
                                     constr, &nullSignaller, state->box,
                                     nullptr, &bSumEkinhOld,
@@ -1240,7 +1250,9 @@ void gmx::Simulator::do_md()
         {
             /* erase F_EKIN and F_TEMP here? */
             /* just compute the kinetic energy at the half step to perform a trotter step */
-            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+            compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                            state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                            mdatoms, nrnb, &vcm,
                             wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                             constr, &nullSignaller, lastbox,
                             nullptr, &bSumEkinhOld,
@@ -1327,7 +1339,9 @@ void gmx::Simulator::do_md()
                 bool                doIntraSimSignal = true;
                 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 
-                compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, &vcm,
+                compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                                state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                                mdatoms, nrnb, &vcm,
                                 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                                 constr, &signaller,
                                 lastbox,
@@ -1341,7 +1355,7 @@ void gmx::Simulator::do_md()
                                 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
                                 );
                 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                                top_global, &top, state,
+                                                top_global, &top, state->x.rvec_array(), state->box,
                                                 &shouldCheckNumberOfBondedInteractions);
             }
         }

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index 9e12af90dc73e6d267c5d8531be8a025438ea5d8..cfb472eac69a16ed9675be099167fea5de7a7201 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -311,13 +311,15 @@ void gmx::Simulator::do_mimic()
                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
         bool   bSumEkinhOld = false;
         t_vcm *vcm          = nullptr;
-        compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+        compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                        state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                        mdatoms, nrnb, vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
     }
     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                    top_global, &top, state,
+                                    top_global, &top, state->x.rvec_array(), state->box,
                                     &shouldCheckNumberOfBondedInteractions);
 
     if (MASTER(cr))
@@ -515,7 +517,9 @@ void gmx::Simulator::do_mimic()
             t_vcm              *vcm              = nullptr;
             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 
-            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+            compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                            state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                            mdatoms, nrnb, vcm,
                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
                             constr, &signaller,
                             state->box,
@@ -524,7 +528,7 @@ void gmx::Simulator::do_mimic()
                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
                             );
             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                            top_global, &top, state,
+                                            top_global, &top, state->x.rvec_array(), state->box,
                                             &shouldCheckNumberOfBondedInteractions);
         }
 

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index cfbbc5a29aa00670d4462386053c363316c9f12a..53db42363e54ee21a677623d45e3d08886825c81 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -381,13 +381,15 @@ void gmx::Simulator::do_rerun()
                              (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
         bool   bSumEkinhOld = false;
         t_vcm *vcm          = nullptr;
-        compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+        compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                        state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                        mdatoms, nrnb, vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
     }
     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                    top_global, &top, state,
+                                    top_global, &top, state->x.rvec_array(), state->box,
                                     &shouldCheckNumberOfBondedInteractions);
 
     if (MASTER(cr))
@@ -637,7 +639,9 @@ void gmx::Simulator::do_rerun()
             t_vcm              *vcm              = nullptr;
             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 
-            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+            compute_globals(fplog, gstat, cr, ir, fr, ekind,
+                            state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
+                            mdatoms, nrnb, vcm,
                             wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                             constr, &signaller,
                             state->box,
@@ -646,7 +650,7 @@ void gmx::Simulator::do_rerun()
                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
                             );
             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
-                                            top_global, &top, state,
+                                            top_global, &top, state->x.rvec_array(), state->box,
                                             &shouldCheckNumberOfBondedInteractions);
         }