Convert t_vcm to C++, plugging a memory leak

[alexxy/gromacs.git] / src / gromacs / mdrun / md.cpp

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 34c5e0b08b4bcbb0d09608032fd3198d895937a3..1d108d726f2045da1cde2261b3aff6063cdcac5d 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -166,7 +166,6 @@ void gmx::Integrator::do_md()
     tensor                  force_vir, shake_vir, total_vir, tmp_vir, pres;
     int                     i, m;
     rvec                    mu_tot;
-    t_vcm                  *vcm;
     matrix                  parrinellorahmanMu, M;
     gmx_repl_ex_t           repl_ex = nullptr;
     gmx_localtop_t          top;
@@ -256,7 +255,7 @@ void gmx::Integrator::do_md()
             &t, &t0, state_global, lam0,
             nrnb, top_global, &upd, deform,
             nfile, fnm, &outf, &mdebin,
-            force_vir, shake_vir, total_vir, pres, mu_tot, &bSimAnn, &vcm, wcycle);
+            force_vir, shake_vir, total_vir, pres, mu_tot, &bSimAnn, wcycle);
 
     /* Energy terms and groups */
     snew(enerd, 1);
@@ -486,6 +485,10 @@ void gmx::Integrator::do_md()
                   | (continuationOptions.haveReadEkin ? CGLO_READEKIN : 0));
 
     bSumEkinhOld = FALSE;
+
+    t_vcm vcm(top_global->groups, *ir);
+    reportComRemovalInfo(fplog, vcm);
+
     /* To minimize communication, compute_globals computes the COM velocity
      * and the kinetic energy for the velocities without COM motion removed.
      * Thus to get the kinetic energy without the COM contribution, we need
@@ -499,7 +502,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags_iteration
@@ -516,7 +519,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                         constr, &nullSignaller, state->box,
                         nullptr, &bSumEkinhOld,
@@ -787,7 +790,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
                             constr, &nullSignaller, state->box,
                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
@@ -935,7 +938,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                                 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                                 constr, &nullSignaller, state->box,
                                 &totalNumberOfBondedInteractions, &bSumEkinhOld,
@@ -990,7 +993,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                                     wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
                                     constr, &nullSignaller, state->box,
                                     nullptr, &bSumEkinhOld,
@@ -1171,7 +1174,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                             wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                             constr, &nullSignaller, lastbox,
                             nullptr, &bSumEkinhOld,
@@ -1258,7 +1261,7 @@ void gmx::Integrator::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, mdatoms, nrnb, &vcm,
                                 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                                 constr, &signaller,
                                 lastbox,