From 9144f57727c4ecbe118c2c776811008574941e73 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Wed, 18 Sep 2024 22:04:56 +0200
Subject: [PATCH] fix a big issue for GMX2024 patch

I do not know how this got lost because it renders the code
unusable
---
 .../gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp   |  8 +++++++-
 .../src/gromacs/mdrun/md.cpp.preplumed             |  1 -
 .../src/gromacs/mdrun/runner.cpp                   | 14 +++++++++-----
 .../src/gromacs/mdrun/runner.cpp.preplumed         | 14 +++++++++-----
 4 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp b/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp
index 18f0bb0ce1..93a608d00e 100644
--- a/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp
+++ b/patches/gromacs-2024.2.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/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp.preplumed b/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp.preplumed
index ed25c89fd8..167f7c6018 100644
--- a/patches/gromacs-2024.2.diff/src/gromacs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-2024.2.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/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp b/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp
index 7dc23d2fe2..572d09fc69 100644
--- a/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp
+++ b/patches/gromacs-2024.2.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/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp.preplumed b/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp.preplumed
index 2e3f56c232..0ff3341b01 100644
--- a/patches/gromacs-2024.2.diff/src/gromacs/mdrun/runner.cpp.preplumed
+++ b/patches/gromacs-2024.2.diff/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)
                 {