Merge branch 'master' into add-value-types

plumed · Sep 26, 2024 · 7223d69 · 7223d69 · PlumedBot · Sep 26, 2024
2 parents c4ce154 + 9045979
commit 7223d69
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Showing 32 changed files with 26 additions and 13 deletions.
diff --git a/patches/gromacs-2024.2.config → patches/gromacs-2024.3.config b/patches/gromacs-2024.2.config → patches/gromacs-2024.3.config
diff --git a/...cs-2024.2.diff/src/gromacs/CMakeLists.txt → ...cs-2024.3.diff/src/gromacs/CMakeLists.txt b/...cs-2024.2.diff/src/gromacs/CMakeLists.txt → ...cs-2024.3.diff/src/gromacs/CMakeLists.txt
diff --git a/...diff/src/gromacs/CMakeLists.txt.preplumed → ...diff/src/gromacs/CMakeLists.txt.preplumed b/...diff/src/gromacs/CMakeLists.txt.preplumed → ...diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/...024.2.diff/src/gromacs/mdlib/expanded.cpp → ...024.3.diff/src/gromacs/mdlib/expanded.cpp b/...024.2.diff/src/gromacs/mdlib/expanded.cpp → ...024.3.diff/src/gromacs/mdlib/expanded.cpp
diff --git a/.../src/gromacs/mdlib/expanded.cpp.preplumed → .../src/gromacs/mdlib/expanded.cpp.preplumed b/.../src/gromacs/mdlib/expanded.cpp.preplumed → .../src/gromacs/mdlib/expanded.cpp.preplumed
diff --git a/...-2024.2.diff/src/gromacs/mdlib/expanded.h → ...-2024.3.diff/src/gromacs/mdlib/expanded.h b/...-2024.2.diff/src/gromacs/mdlib/expanded.h → ...-2024.3.diff/src/gromacs/mdlib/expanded.h
diff --git a/...ff/src/gromacs/mdlib/expanded.h.preplumed → ...ff/src/gromacs/mdlib/expanded.h.preplumed b/...ff/src/gromacs/mdlib/expanded.h.preplumed → ...ff/src/gromacs/mdlib/expanded.h.preplumed
diff --git a/...024.2.diff/src/gromacs/mdlib/sim_util.cpp → ...024.3.diff/src/gromacs/mdlib/sim_util.cpp b/...024.2.diff/src/gromacs/mdlib/sim_util.cpp → ...024.3.diff/src/gromacs/mdlib/sim_util.cpp
diff --git a/.../src/gromacs/mdlib/sim_util.cpp.preplumed → .../src/gromacs/mdlib/sim_util.cpp.preplumed b/.../src/gromacs/mdlib/sim_util.cpp.preplumed → .../src/gromacs/mdlib/sim_util.cpp.preplumed
diff --git a/.../src/gromacs/mdrun/legacymdrunoptions.cpp → .../src/gromacs/mdrun/legacymdrunoptions.cpp b/.../src/gromacs/mdrun/legacymdrunoptions.cpp → .../src/gromacs/mdrun/legacymdrunoptions.cpp
diff --git a/...cs/mdrun/legacymdrunoptions.cpp.preplumed → ...cs/mdrun/legacymdrunoptions.cpp.preplumed b/...cs/mdrun/legacymdrunoptions.cpp.preplumed → ...cs/mdrun/legacymdrunoptions.cpp.preplumed
diff --git a/...ff/src/gromacs/mdrun/legacymdrunoptions.h → ...ff/src/gromacs/mdrun/legacymdrunoptions.h b/...ff/src/gromacs/mdrun/legacymdrunoptions.h → ...ff/src/gromacs/mdrun/legacymdrunoptions.h
diff --git a/...macs/mdrun/legacymdrunoptions.h.preplumed → ...macs/mdrun/legacymdrunoptions.h.preplumed b/...macs/mdrun/legacymdrunoptions.h.preplumed → ...macs/mdrun/legacymdrunoptions.h.preplumed
diff --git a/...macs-2024.2.diff/src/gromacs/mdrun/md.cpp → ...macs-2024.3.diff/src/gromacs/mdrun/md.cpp b/...macs-2024.2.diff/src/gromacs/mdrun/md.cpp → ...macs-2024.3.diff/src/gromacs/mdrun/md.cpp
@@ -1089,6 +1089,13 @@ void gmx::LegacySimulator::do_md()
                                     do_verbose && !bPMETunePrinting);
                 upd.updateAfterPartition(state_->numAtoms(), md->cFREEZE, md->cTC, md->cACC);
                 fr_->longRangeNonbondeds->updateAfterPartition(*md);
+                /* PLUMED */
+                if(plumedswitch){
+                  int nat_home = dd_numHomeAtoms(*cr_->dd);
+                  plumed_cmd(plumedmain,"setAtomsNlocal",&nat_home);
+                  plumed_cmd(plumedmain,"setAtomsGatindex",cr_->dd->globalAtomIndices.data());
+                }
+                /* END PLUMED */
             }
         }
 
@@ -1721,7 +1728,6 @@ void gmx::LegacySimulator::do_md()
                 trotter_update(ir,
                                step,
                                ekind_,
-                               enerd_,
                                state_,
                                total_vir,
                                md->homenr,

diff --git a/...2.diff/src/gromacs/mdrun/md.cpp.preplumed → ...3.diff/src/gromacs/mdrun/md.cpp.preplumed b/...2.diff/src/gromacs/mdrun/md.cpp.preplumed → ...3.diff/src/gromacs/mdrun/md.cpp.preplumed
@@ -1480,7 +1480,6 @@ void gmx::LegacySimulator::do_md()
                 trotter_update(ir,
                                step,
                                ekind_,
-                               enerd_,
                                state_,
                                total_vir,
                                md->homenr,

diff --git a/...024.2.diff/src/gromacs/mdrun/minimize.cpp → ...024.3.diff/src/gromacs/mdrun/minimize.cpp b/...024.2.diff/src/gromacs/mdrun/minimize.cpp → ...024.3.diff/src/gromacs/mdrun/minimize.cpp
diff --git a/.../src/gromacs/mdrun/minimize.cpp.preplumed → .../src/gromacs/mdrun/minimize.cpp.preplumed b/.../src/gromacs/mdrun/minimize.cpp.preplumed → .../src/gromacs/mdrun/minimize.cpp.preplumed
diff --git a/...iff/src/gromacs/mdrun/replicaexchange.cpp → ...iff/src/gromacs/mdrun/replicaexchange.cpp b/...iff/src/gromacs/mdrun/replicaexchange.cpp → ...iff/src/gromacs/mdrun/replicaexchange.cpp
diff --git a/...omacs/mdrun/replicaexchange.cpp.preplumed → ...omacs/mdrun/replicaexchange.cpp.preplumed b/...omacs/mdrun/replicaexchange.cpp.preplumed → ...omacs/mdrun/replicaexchange.cpp.preplumed
diff --git a/....diff/src/gromacs/mdrun/replicaexchange.h → ....diff/src/gromacs/mdrun/replicaexchange.h b/....diff/src/gromacs/mdrun/replicaexchange.h → ....diff/src/gromacs/mdrun/replicaexchange.h
diff --git a/...gromacs/mdrun/replicaexchange.h.preplumed → ...gromacs/mdrun/replicaexchange.h.preplumed b/...gromacs/mdrun/replicaexchange.h.preplumed → ...gromacs/mdrun/replicaexchange.h.preplumed
diff --git a/...s-2024.2.diff/src/gromacs/mdrun/rerun.cpp → ...s-2024.3.diff/src/gromacs/mdrun/rerun.cpp b/...s-2024.2.diff/src/gromacs/mdrun/rerun.cpp → ...s-2024.3.diff/src/gromacs/mdrun/rerun.cpp
diff --git a/...iff/src/gromacs/mdrun/rerun.cpp.preplumed → ...iff/src/gromacs/mdrun/rerun.cpp.preplumed b/...iff/src/gromacs/mdrun/rerun.cpp.preplumed → ...iff/src/gromacs/mdrun/rerun.cpp.preplumed
diff --git a/...-2024.2.diff/src/gromacs/mdrun/runner.cpp → ...-2024.3.diff/src/gromacs/mdrun/runner.cpp b/...-2024.2.diff/src/gromacs/mdrun/runner.cpp → ...-2024.3.diff/src/gromacs/mdrun/runner.cpp
@@ -2248,11 +2248,15 @@ int Mdrunner::mdrunner()
                         deviceStreamManager->context(),
                         deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
                         wcycle.get());
-                fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
-                        std::make_unique<gmx::GpuForceReduction>(
-                                deviceStreamManager->context(),
-                                deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
-                                wcycle.get());
+
+                if (runScheduleWork.simulationWork.havePpDomainDecomposition)
+                {
+                    fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
+                            std::make_unique<gmx::GpuForceReduction>(
+                                    deviceStreamManager->context(),
+                                    deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
+                                    wcycle.get());
+                }
 
                 if (runScheduleWork.simulationWork.useMdGpuGraph)
                 {

diff --git a/...ff/src/gromacs/mdrun/runner.cpp.preplumed → ...ff/src/gromacs/mdrun/runner.cpp.preplumed b/...ff/src/gromacs/mdrun/runner.cpp.preplumed → ...ff/src/gromacs/mdrun/runner.cpp.preplumed
@@ -2234,11 +2234,15 @@ int Mdrunner::mdrunner()
                         deviceStreamManager->context(),
                         deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal),
                         wcycle.get());
-                fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
-                        std::make_unique<gmx::GpuForceReduction>(
-                                deviceStreamManager->context(),
-                                deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
-                                wcycle.get());
+
+                if (runScheduleWork.simulationWork.havePpDomainDecomposition)
+                {
+                    fr->gpuForceReduction[gmx::AtomLocality::NonLocal] =
+                            std::make_unique<gmx::GpuForceReduction>(
+                                    deviceStreamManager->context(),
+                                    deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal),
+                                    wcycle.get());
+                }
 
                 if (runScheduleWork.simulationWork.useMdGpuGraph)
                 {

diff --git a/...ularsimulator/expandedensembleelement.cpp → ...ularsimulator/expandedensembleelement.cpp b/...ularsimulator/expandedensembleelement.cpp → ...ularsimulator/expandedensembleelement.cpp
diff --git a/...tor/expandedensembleelement.cpp.preplumed → ...tor/expandedensembleelement.cpp.preplumed b/...tor/expandedensembleelement.cpp.preplumed → ...tor/expandedensembleelement.cpp.preplumed
diff --git a/...gromacs/taskassignment/decidegpuusage.cpp → ...gromacs/taskassignment/decidegpuusage.cpp b/...gromacs/taskassignment/decidegpuusage.cpp → ...gromacs/taskassignment/decidegpuusage.cpp
diff --git a/...skassignment/decidegpuusage.cpp.preplumed → ...skassignment/decidegpuusage.cpp.preplumed b/...skassignment/decidegpuusage.cpp.preplumed → ...skassignment/decidegpuusage.cpp.preplumed
diff --git a/...e/gromacs/taskassignment/decidegpuusage.h → ...e/gromacs/taskassignment/decidegpuusage.h b/...e/gromacs/taskassignment/decidegpuusage.h → ...e/gromacs/taskassignment/decidegpuusage.h
diff --git a/...taskassignment/decidegpuusage.h.preplumed → ...taskassignment/decidegpuusage.h.preplumed b/...taskassignment/decidegpuusage.h.preplumed → ...taskassignment/decidegpuusage.h.preplumed
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
@@ -113,7 +113,7 @@ s(r) = 1 - \tanh\left( \frac{ r - d_0 }{ r_0 } \right)
 \f$s(r) =\left\{\begin{array}{ll}
    1                                                           & \mathrm{if } r \leq d_0 \\
    0.5 \left( \cos ( \frac{ r - d_0 }{ r_0 } \pi ) + 1 \right) & \mathrm{if } d_0 < r\leq d_0 + r_0 \\
-   0                                                           & \mathrm{if } r < d_0 + r_0
+   0                                                           & \mathrm{if } r > d_0 + r_0
   \end{array}\right.
 \f$
 </td> <td>
-Original file line number
+Diff line change
@@ Expand Up / @@ -1480,7 +1480,6 @@ void gmx::LegacySimulator::do_md() @@
                     trotter_update(ir,
                                    step,
                                    ekind_,
-                                   enerd_,
                                    state_,
                                    total_vir,
                                    md->homenr,
@@ Expand Down @@