Constructor for gmx_ekindata_t

Moved init_ekin_data from tgroup header/source to group and made
it the constructor for gmx_ekindata_t. Also made gmx_ekindata_t a
class since the number of threads is only needed by constructor
and destructor and can thus be private. Further refactoring of
members of gmx_ekindata_t would eliminate the need for the nthreads
data member entirely. Other members we not made private to avoid a
ripple of changes adding "()" to numerous lines in several files.

diff --git a/src/gromacs/mdlib/coupling.h b/src/gromacs/mdlib/coupling.h
index 7f8d3c5a2617aacbccd7355acb5a9473aa39b72c..affd45bd44fc6d2959617b691d1756b35d43af12 100644 (file)
--- a/src/gromacs/mdlib/coupling.h
+++ b/src/gromacs/mdlib/coupling.h
@@ -45,7 +45,7 @@
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct t_commrec;
 struct t_extmass;

diff --git a/src/gromacs/mdlib/energyoutput.h b/src/gromacs/mdlib/energyoutput.h
index 902ad5b81131bf2affce9deab3b1c9c32b71f13c..ea917b6e0215c152458b4c8e7f2018ce15c27e25 100644 (file)
--- a/src/gromacs/mdlib/energyoutput.h
+++ b/src/gromacs/mdlib/energyoutput.h
@@ -53,7 +53,7 @@
 
 class energyhistory_t;
 struct ener_file;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct SimulationGroups;
 struct gmx_mtop_t;

diff --git a/src/gromacs/mdlib/md_support.h b/src/gromacs/mdlib/md_support.h
index 1975239425dbbbb5b37b2e7766d65f5aafb98ae4..40e1437c13beeef9e176dc4e5fc01b58a39b2cad 100644 (file)
--- a/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -42,7 +42,7 @@
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/timing/wallcycle.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_global_stat;
 struct gmx_signalling_t;

diff --git a/src/gromacs/mdlib/stat.h b/src/gromacs/mdlib/stat.h
index 03687279e4070e681c41b8a3e85c6bae3a5fb691..8001bf0d39605ea27d69fff2864f3f4bfe075441 100644 (file)
--- a/src/gromacs/mdlib/stat.h
+++ b/src/gromacs/mdlib/stat.h
@@ -43,7 +43,7 @@
 
 #include "gromacs/math/vectypes.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct t_vcm;
 struct t_inputrec;

diff --git a/src/gromacs/mdlib/tests/energyoutput.cpp b/src/gromacs/mdlib/tests/energyoutput.cpp
index fac276b9f65285b5f61a53fe232234ea81356dc4..78a4d923673887da5b465cc91a8fc603b93bb030 100644 (file)
--- a/src/gromacs/mdlib/tests/energyoutput.cpp
+++ b/src/gromacs/mdlib/tests/energyoutput.cpp
@@ -138,6 +138,9 @@ const EnergyOutputTestParameters parametersSets[] = {
  */
 class EnergyOutputTest : public ::testing::TestWithParam<EnergyOutputTestParameters>
 {
+    int  numTempCouplingGroups_ = 3;
+    real cosAccel_              = 1.0;
+
 public:
     //! File manager
     TestFileManager fileManager_;
@@ -193,6 +196,7 @@ public:
     TestReferenceChecker checker_;
 
     EnergyOutputTest() :
+        ekindata_(numTempCouplingGroups_, cosAccel_, 1),
         logFilename_(fileManager_.getTemporaryFilePath(".log")),
         edrFilename_(fileManager_.getTemporaryFilePath(".edr")),
         log_(std::fopen(logFilename_.c_str(), "w")),
@@ -312,12 +316,12 @@ public:
             mtop_.groups.groupNames.emplace_back(&handle);
         }
 
-        mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(3);
+        mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput].resize(numTempCouplingGroups_);
         mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][0] = 0;
         mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][1] = 1;
         mtop_.groups.groups[SimulationAtomGroupType::EnergyOutput][2] = 2;
 
-        mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(3);
+        mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].resize(numTempCouplingGroups_);
         mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][0] = 0;
         mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][1] = 1;
         mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling][2] = 2;
@@ -344,15 +348,10 @@ public:
         ekindata_.tcstat.resize(mtop_.groups.groups[SimulationAtomGroupType::TemperatureCoupling].size());
 
         // This is needed so that the ebin space will be allocated
-        inputrec_.cos_accel = 1.0;
-        // This is to keep the destructor happy (otherwise sfree() segfaults)
-        ekindata_.nthreads = 0;
-        snew(ekindata_.ekin_work_alloc, 1);
-        snew(ekindata_.ekin_work, 1);
-        snew(ekindata_.dekindl_work, 1);
+        inputrec_.cos_accel = cosAccel_;
 
         // Group options for annealing output
-        inputrec_.opts.ngtc = 3;
+        inputrec_.opts.ngtc = numTempCouplingGroups_;
         snew(inputrec_.opts.ref_t, inputrec_.opts.ngtc);
         snew(inputrec_.opts.annealing, inputrec_.opts.ngtc);
         inputrec_.opts.annealing[0] = SimulatedAnnealing::No;

diff --git a/src/gromacs/mdlib/tests/leapfrogtestdata.cpp b/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
index 8ae0a74051978cfad7bb8a18b3bcb572f2a1cbf9..c00fbbd4c001e0aa4bae2419286fddcf215a931f 100644 (file)
--- a/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
+++ b/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
@@ -83,6 +83,7 @@ LeapFrogTestData::LeapFrogTestData(int        numAtoms,
     f_(numAtoms),
     inverseMasses_(numAtoms),
     inverseMassesPerDim_(numAtoms),
+    kineticEnergyData_(numTCoupleGroups == 0 ? 1 : numTCoupleGroups, 0.0, 1),
     numTCoupleGroups_(numTCoupleGroups)
 {
     mdAtoms_.nr = numAtoms_;
@@ -128,10 +129,9 @@ LeapFrogTestData::LeapFrogTestData(int        numAtoms,
         {
             mdAtoms_.cTC[i] = 0;
         }
-        kineticEnergyData_.ngtc = 1;
         t_grp_tcstat temperatureCouplingGroupData;
         temperatureCouplingGroupData.lambda = 1.0;
-        kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+        kineticEnergyData_.tcstat[0]        = temperatureCouplingGroupData;
     }
     else
     {
@@ -140,13 +140,12 @@ LeapFrogTestData::LeapFrogTestData(int        numAtoms,
         {
             mdAtoms_.cTC[i] = i % numTCoupleGroups_;
         }
-        kineticEnergyData_.ngtc = numTCoupleGroups_;
-        for (int i = 0; i < numTCoupleGroups; i++)
+        for (int i = 0; i < numTCoupleGroups_; i++)
         {
             real         tCoupleLambda = 1.0 - (i + 1.0) / 10.0;
             t_grp_tcstat temperatureCouplingGroupData;
             temperatureCouplingGroupData.lambda = tCoupleLambda;
-            kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+            kineticEnergyData_.tcstat[i]        = temperatureCouplingGroupData;
         }
     }
 
@@ -167,13 +166,6 @@ LeapFrogTestData::LeapFrogTestData(int        numAtoms,
     state_.box[ZZ][YY] = 0.0;
     state_.box[ZZ][ZZ] = 10.0;
 
-    kineticEnergyData_.cosacc.cos_accel = 0.0;
-
-    kineticEnergyData_.nthreads = 1;
-    snew(kineticEnergyData_.ekin_work_alloc, kineticEnergyData_.nthreads);
-    snew(kineticEnergyData_.ekin_work, kineticEnergyData_.nthreads);
-    snew(kineticEnergyData_.dekindl_work, kineticEnergyData_.nthreads);
-
     mdAtoms_.homenr                   = numAtoms_;
     mdAtoms_.haveVsites               = false;
     mdAtoms_.havePartiallyFrozenAtoms = false;

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index 1fccc924fe055c59910913ad91ba9c577fc2ff33..f86fc068b109b2fd29709ab31583ca9233665083 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -40,70 +40,11 @@
 
 #include "tgroup.h"
 
-#include <cmath>
-
-#include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/coupling.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/rbin.h"
 #include "gromacs/mdtypes/group.h"
 #include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-
-void init_ekindata(FILE gmx_unused* log, const t_grpopts* opts, gmx_ekindata_t* ekind, real cos_accel)
-{
-    int i;
-
-    ekind->ngtc = opts->ngtc;
-    ekind->tcstat.resize(opts->ngtc);
-    /* Set Berendsen tcoupl lambda's to 1,
-     * so runs without Berendsen coupling are not affected.
-     */
-    for (i = 0; i < opts->ngtc; i++)
-    {
-        ekind->tcstat[i].lambda         = 1.0;
-        ekind->tcstat[i].vscale_nhc     = 1.0;
-        ekind->tcstat[i].ekinscaleh_nhc = 1.0;
-        ekind->tcstat[i].ekinscalef_nhc = 1.0;
-    }
 
-    int nthread     = gmx_omp_nthreads_get(emntUpdate);
-    ekind->nthreads = nthread;
-    snew(ekind->ekin_work_alloc, nthread);
-    snew(ekind->ekin_work, nthread);
-    snew(ekind->dekindl_work, nthread);
-#pragma omp parallel for num_threads(nthread) schedule(static)
-    for (int thread = 0; thread < nthread; thread++)
-    {
-        try
-        {
-#define EKIN_WORK_BUFFER_SIZE 2
-            /* Allocate 2 extra elements on both sides, so in single
-             * precision we have
-             * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
-             * buffer on both sides to avoid cache pollution.
-             */
-            snew(ekind->ekin_work_alloc[thread], ekind->ngtc + 2 * EKIN_WORK_BUFFER_SIZE);
-            ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
-            /* Nasty hack so we can have the per-thread accumulation
-             * variable for dekindl in the same thread-local cache lines
-             * as the per-thread accumulation tensors for ekin[fh],
-             * because they are accumulated in the same loop. */
-            ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
-#undef EKIN_WORK_BUFFER_SIZE
-        }
-        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
-    }
-
-    ekind->cosacc.cos_accel = cos_accel;
-}
 
 real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
 {

diff --git a/src/gromacs/mdlib/tgroup.h b/src/gromacs/mdlib/tgroup.h
index 1f9189414a5ad038ef0e8259f9887ebb22d818e8..9a62f8fe0e3328bb0c5ce4e7599ea296ce6d1de2 100644 (file)
--- a/src/gromacs/mdlib/tgroup.h
+++ b/src/gromacs/mdlib/tgroup.h
@@ -37,23 +37,12 @@
 #ifndef GMX_MDLIB_TGROUP_H
 #define GMX_MDLIB_TGROUP_H
 
-#include <cstdio>
-
-#include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-struct gmx_ekindata_t;
-struct t_commrec;
+class gmx_ekindata_t;
 struct t_grpopts;
-struct t_mdatoms;
-
-void init_ekindata(FILE* log, const t_grpopts* opts, gmx_ekindata_t* ekind, real cos_accel);
-/* Allocate memory and set the grpnr array. */
-
-void done_ekindata(gmx_ekindata_t* ekind);
-/* Free the memory */
 
-real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, gmx_bool bEkinFullStep, gmx_bool bScaleEkin);
+real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, bool bEkinFullStep, bool bScaleEkin);
 /* Sum the group ekins into total ekin and calc temp per group,
  * return total temperature.
  */

diff --git a/src/gromacs/mdlib/trajectory_writing.h b/src/gromacs/mdlib/trajectory_writing.h
index 5d60396834b271ae15a046eb58498368ff4cc002..220b6056eb0a12e6bd3ff9ef355083720a1c8305 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.h
+++ b/src/gromacs/mdlib/trajectory_writing.h
@@ -44,7 +44,7 @@
 #include "gromacs/mdlib/mdoutf.h"
 #include "gromacs/timing/wallcycle.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_mtop_t;
 struct ObservablesHistory;
 struct t_commrec;

diff --git a/src/gromacs/mdlib/update.h b/src/gromacs/mdlib/update.h
index 207685f19e7ae4336678fa85ff1e0b2bda9a7661..1e7a5d530ff9559b561f73a776fbc7f2b2d2d938 100644 (file)
--- a/src/gromacs/mdlib/update.h
+++ b/src/gromacs/mdlib/update.h
@@ -49,7 +49,7 @@
 #include "gromacs/utility/real.h"
 
 class ekinstate_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 enum class PbcType;
 struct t_fcdata;

diff --git a/src/gromacs/mdlib/update_vv.h b/src/gromacs/mdlib/update_vv.h
index b1d7cf00ae74502e1891f5cd4e6a6b9b3d498590..ddc4f8b747f3c7d475c235f68a7cc18ccfb8bccc 100644 (file)
--- a/src/gromacs/mdlib/update_vv.h
+++ b/src/gromacs/mdlib/update_vv.h
@@ -44,7 +44,7 @@
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/mdtypes/md_enums.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_global_stat;
 struct gmx_localtop_t;

diff --git a/src/gromacs/mdrun/isimulator.h b/src/gromacs/mdrun/isimulator.h
index 6e9c6c614992b83188cb27f71bc49c6dd365153e..7ef5a998466122d140a4b3fb17dc6380f13b71dc 100644 (file)
--- a/src/gromacs/mdrun/isimulator.h
+++ b/src/gromacs/mdrun/isimulator.h
@@ -44,7 +44,7 @@
 #include "gromacs/mdlib/stophandler.h"
 
 class energyhistory_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_enfrot;
 struct gmx_mtop_t;

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index f732c60ede37c85914da1450daac5590bc5d7db7..19fe21674740d6cc620f5a31a2e7191ba089ae66 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -1868,8 +1868,7 @@ int Mdrunner::mdrunner()
                            "cos_acceleration is only supported by integrator=md");
 
         /* Kinetic energy data */
-        gmx_ekindata_t ekind;
-        init_ekindata(fplog, &(inputrec->opts), &ekind, inputrec->cos_accel);
+        gmx_ekindata_t ekind(inputrec->opts.ngtc, inputrec->cos_accel, gmx_omp_nthreads_get(emntUpdate));
 
         /* Set up interactive MD (IMD) */
         auto imdSession = makeImdSession(inputrec.get(),

diff --git a/src/gromacs/mdrun/simulatorbuilder.h b/src/gromacs/mdrun/simulatorbuilder.h
index 3bd22bb769686a6d232899fdbf21e9036c8a7659..624f8d8e7135069ba802fe7e51a88a3c0a902e09 100644 (file)
--- a/src/gromacs/mdrun/simulatorbuilder.h
+++ b/src/gromacs/mdrun/simulatorbuilder.h
@@ -45,7 +45,7 @@
 
 
 class energyhistory_t;
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_enfrot;
 struct gmx_mtop_t;

diff --git a/src/gromacs/mdtypes/group.cpp b/src/gromacs/mdtypes/group.cpp
index b0c15ca8525b9ce873f998b634cf89f8e1055c17..8e708c737d7be5e818ba77b8ab25f461375ab014 100644 (file)
--- a/src/gromacs/mdtypes/group.cpp
+++ b/src/gromacs/mdtypes/group.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, 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.
@@ -43,9 +43,56 @@
 
 #include "group.h"
 
+#include "gromacs/utility/exceptions.h"
+
+gmx_ekindata_t::gmx_ekindata_t(int numTempCoupleGroups, real cos_accel, int numThreads) :
+    ngtc(numTempCoupleGroups),
+    nthreads_(numThreads)
+{
+    tcstat.resize(ngtc);
+    /* Set Berendsen tcoupl lambda's to 1,
+     * so runs without Berendsen coupling are not affected.
+     */
+    for (int i = 0; i < ngtc; i++)
+    {
+        tcstat[i].lambda         = 1.0;
+        tcstat[i].vscale_nhc     = 1.0;
+        tcstat[i].ekinscaleh_nhc = 1.0;
+        tcstat[i].ekinscalef_nhc = 1.0;
+    }
+
+    snew(ekin_work_alloc, nthreads_);
+    snew(ekin_work, nthreads_);
+    snew(dekindl_work, nthreads_);
+
+#pragma omp parallel for num_threads(nthreads_) schedule(static)
+    for (int thread = 0; thread < nthreads_; thread++)
+    {
+        try
+        {
+            constexpr int EKIN_WORK_BUFFER_SIZE = 2;
+            /* Allocate 2 extra elements on both sides, so in single
+             * precision we have
+             * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
+             * buffer on both sides to avoid cache pollution.
+             */
+            snew(ekin_work_alloc[thread], ngtc + 2 * EKIN_WORK_BUFFER_SIZE);
+            ekin_work[thread] = ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
+            /* Nasty hack so we can have the per-thread accumulation
+             * variable for dekindl in the same thread-local cache lines
+             * as the per-thread accumulation tensors for ekin[fh],
+             * because they are accumulated in the same loop. */
+            dekindl_work[thread] = &(ekin_work[thread][ngtc][0][0]);
+        }
+        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+    }
+
+    cosacc.cos_accel = cos_accel;
+}
+
 gmx_ekindata_t::~gmx_ekindata_t()
 {
-    for (int i = 0; i < nthreads; i++)
+    for (int i = 0; i < nthreads_; i++)
     {
         sfree(ekin_work_alloc[i]);
     }

diff --git a/src/gromacs/mdtypes/group.h b/src/gromacs/mdtypes/group.h
index 49ece654769edb682353bd9de5c0c4b73af79a1b..27ebd8e1be21fc67d5f780f55748917960a9efe2 100644 (file)
--- a/src/gromacs/mdtypes/group.h
+++ b/src/gromacs/mdtypes/group.h
@@ -75,12 +75,12 @@ struct t_cos_acc
     real vcos = 0;
 };
 
-struct gmx_ekindata_t
+class gmx_ekindata_t
 {
+public:
+    gmx_ekindata_t(int numTempCoupleGroups, real cos_accel, int numThreads);
     //! The number of T-coupling groups
-    int ngtc = 0;
-    //! For size of ekin_work
-    int nthreads = 0;
+    int ngtc;
     //! T-coupling data
     std::vector<t_grp_tcstat> tcstat;
     //! Allocated locations for *_work members
@@ -101,6 +101,10 @@ struct gmx_ekindata_t
     t_cos_acc cosacc;
 
     ~gmx_ekindata_t();
+
+private:
+    //! For size of ekin_work
+    int nthreads_ = 0;
 };
 
 #define GID(igid, jgid, gnr) \

diff --git a/src/gromacs/modularsimulator/energydata.h b/src/gromacs/modularsimulator/energydata.h
index bc0c55dc3081cf32c004721217ee7d9ee1a2b507..0020dd04da771c4d84b81830fdc548b20f2c5ed0 100644 (file)
--- a/src/gromacs/modularsimulator/energydata.h
+++ b/src/gromacs/modularsimulator/energydata.h
@@ -49,7 +49,7 @@
 
 #include "modularsimulatorinterfaces.h"
 
-struct gmx_ekindata_t;
+class gmx_ekindata_t;
 struct gmx_enerdata_t;
 struct gmx_mtop_t;
 struct ObservablesHistory;