Move ownership of kinetic energy object to ISimulator

Treating the kinetic energy object (ekind) equivalently to the
energy object (enerd) makes subsequent changes easier. It also
removes some code duplication between do_md, do_rerun and
do_mimic. There are some algorithms that never use the kinetic
energy (e.g. minimization), but this is true for other members
of ISimulator as well.

Change-Id: I995d14652dae25bcbcaa0a75437382a053e76f74

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index b3a5c80e943f39056b8e12897dbc07e80a32f2ad..d70d7ad3d5408cbb080e4e0551047932f681cedb 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -79,7 +79,7 @@ static void init_grpstat(const gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
 }
 
 void init_ekindata(FILE gmx_unused *log, const gmx_mtop_t *mtop, const t_grpopts *opts,
-                   gmx_ekindata_t *ekind)
+                   gmx_ekindata_t *ekind, real cos_accel)
 {
     int i;
     int nthread, thread;
@@ -135,6 +135,8 @@ void init_ekindata(FILE gmx_unused *log, const gmx_mtop_t *mtop, const t_grpopts
     ekind->ngacc = opts->ngacc;
     ekind->grpstat.resize(opts->ngacc);
     init_grpstat(mtop, opts->ngacc, ekind->grpstat.data());
+
+    ekind->cosacc.cos_accel = cos_accel;
 }
 
 void accumulate_u(const t_commrec *cr, const t_grpopts *opts, gmx_ekindata_t *ekind)

diff --git a/src/gromacs/mdlib/tgroup.h b/src/gromacs/mdlib/tgroup.h
index 3530fe6f813dc8149b78c93af975a263e829cba5..274b077914ff7e4e9394b1cfd888480206ea358f 100644 (file)
--- a/src/gromacs/mdlib/tgroup.h
+++ b/src/gromacs/mdlib/tgroup.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,8 @@ struct t_mdatoms;
 
 void init_ekindata(FILE *log, const gmx_mtop_t *mtop,
                    const t_grpopts *opts,
-                   gmx_ekindata_t *ekind);
+                   gmx_ekindata_t *ekind,
+                   real cos_accel);
 /* Allocate memory and set the grpnr array. */
 
 void done_ekindata(gmx_ekindata_t *ekind);

diff --git a/src/gromacs/mdrun/isimulator.h b/src/gromacs/mdrun/isimulator.h
index 2a8110b1da7d4db680351d968de248b642a69f04..9fbb343514b4571905283f7803cf4955148c39e4 100644 (file)
--- a/src/gromacs/mdrun/isimulator.h
+++ b/src/gromacs/mdrun/isimulator.h
@@ -44,6 +44,7 @@
 #include "gromacs/mdlib/stophandler.h"
 
 class energyhistory_t;
+struct gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_enfrot;
 struct gmx_mtop_t;
@@ -125,6 +126,7 @@ class ISimulator
             gmx_wallcycle                      *wcycle,
             t_forcerec                         *fr,
             gmx_enerdata_t                     *enerd,
+            gmx_ekindata_t                     *ekind,
             PpForceWorkload                    *ppForceWorkload,
             const ReplicaExchangeParameters    &replExParams,
             gmx_membed_t                       *membed,
@@ -158,6 +160,7 @@ class ISimulator
             wcycle(wcycle),
             fr(fr),
             enerd(enerd),
+            ekind(ekind),
             ppForceWorkload(ppForceWorkload),
             replExParams(replExParams),
             membed(membed),
@@ -221,6 +224,8 @@ class ISimulator
         t_forcerec                         *fr;
         //! Data for energy output.
         gmx_enerdata_t                     *enerd;
+        //! Kinetic energy data.
+        gmx_ekindata_t                     *ekind;
         //! Schedule of force-calculation work each step for this task.
         PpForceWorkload                    *ppForceWorkload;
         //! Parameters for replica exchange algorihtms.

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 167ad8a2fb44042350c0d0989def268467c99cd8..fb3bd42d4a5af6c9fe3ed26767a315dd9e631722 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -260,13 +260,6 @@ void gmx::LegacySimulator::do_md()
                                          StartingBehavior::NewSimulation);
     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), false);
 
-    /* Kinetic energy data */
-    std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
-    gmx_ekindata_t                 *ekind    = eKinData.get();
-    init_ekindata(fplog, top_global, &(ir->opts), ekind);
-    /* Copy the cos acceleration to the groups struct */
-    ekind->cosacc.cos_accel = ir->cos_accel;
-
     gstat = global_stat_init(ir);
 
     /* Check for polarizable models and flexible constraints */

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index bfd709a0225e65e22dd3d5d3cc46c625b38cc931..703e1e792464fbf9e3dc1e130c398496318094bc 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -230,13 +230,6 @@ void gmx::LegacySimulator::do_mimic()
                                           StartingBehavior::NewSimulation);
     gmx::EnergyOutput  energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
 
-    /* Kinetic energy data */
-    std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
-    gmx_ekindata_t                 *ekind    = eKinData.get();
-    init_ekindata(fplog, top_global, &(ir->opts), ekind);
-    /* Copy the cos acceleration to the groups struct */
-    ekind->cosacc.cos_accel = ir->cos_accel;
-
     gstat = global_stat_init(ir);
 
     /* Check for polarizable models and flexible constraints */

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index eb31c8a309b7d30feded2214336c39c4462e6fbb..d3937bf09b82f96f19e53ddb91ded81bf94fc54b 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -302,13 +302,6 @@ void gmx::LegacySimulator::do_rerun()
                                          StartingBehavior::NewSimulation);
     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
 
-    /* Kinetic energy data */
-    std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
-    gmx_ekindata_t                 *ekind    = eKinData.get();
-    init_ekindata(fplog, top_global, &(ir->opts), ekind);
-    /* Copy the cos acceleration to the groups struct */
-    ekind->cosacc.cos_accel = ir->cos_accel;
-
     gstat = global_stat_init(ir);
 
     /* Check for polarizable models and flexible constraints */

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 7f0c26fd7fdad261db9a2b4815f5b0c4972ec438..deef8f5b9e72b132f9ebcdc49315cfffb039b177 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -108,6 +108,7 @@
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/group.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdrunoptions.h"
@@ -1467,6 +1468,10 @@ int Mdrunner::mdrunner()
         /* Energy terms and groups */
         gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(), inputrec->fepvals->n_lambda);
 
+        /* Kinetic energy data */
+        gmx_ekindata_t ekind;
+        init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);
+
         /* Set up interactive MD (IMD) */
         auto imdSession = makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
                                          MASTER(cr) ? globalState->x.rvec_array() : nullptr,
@@ -1510,6 +1515,7 @@ int Mdrunner::mdrunner()
                     &observablesHistory,
                     mdAtoms.get(), &nrnb, wcycle, fr,
                     &enerd,
+                    &ekind,
                     &ppForceWorkload,
                     replExParams,
                     membed,