From 66840c9e4f4e264691fe57e60c8fc04d69e8ba91 Mon Sep 17 00:00:00 2001
From: Sophie Blondel <sblondel@utk.edu>
Date: Wed, 29 Jan 2025 15:02:09 -0500
Subject: [PATCH] Free memory before starting a new loop (#206).

---
 xolotl/core/include/xolotl/core/network/Reaction.h | 5 +++--
 xolotl/solver/src/PetscSolver.cpp                  | 9 +++++++++
 xolotl/solver/src/monitor/PetscMonitor1D.cpp       | 3 +++
 xolotl/util/include/xolotl/util/Atomics.h          | 6 +++---
 4 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/xolotl/core/include/xolotl/core/network/Reaction.h b/xolotl/core/include/xolotl/core/network/Reaction.h
index 3e90fe81..cd8112bc 100644
--- a/xolotl/core/include/xolotl/core/network/Reaction.h
+++ b/xolotl/core/include/xolotl/core/network/Reaction.h
@@ -19,7 +19,8 @@ namespace core
 {
 namespace network
 {
-template <typename TImpl> class ReactionNetwork;
+template <typename TImpl>
+class ReactionNetwork;
 /**
  * @brief General reaction class where
  * reactants become products with a given rate
@@ -30,7 +31,7 @@ template <typename TImpl> class ReactionNetwork;
 template <typename TNetwork, typename TDerived>
 class Reaction
 {
-    friend class ReactionNetwork<TNetwork>;
+	friend class ReactionNetwork<TNetwork>;
 	using Types = detail::ReactionNetworkTypes<TNetwork>;
 	using Props = detail::ReactionNetworkProperties<TNetwork>;
 
diff --git a/xolotl/solver/src/PetscSolver.cpp b/xolotl/solver/src/PetscSolver.cpp
index 82fa4a22..1700f66b 100644
--- a/xolotl/solver/src/PetscSolver.cpp
+++ b/xolotl/solver/src/PetscSolver.cpp
@@ -177,6 +177,13 @@ PetscSolver::initialize(int loop, double time, DM oldDA, Vec oldC)
 		PetscCallVoid(PetscInitialize(NULL, NULL, NULL, help));
 		petscInitializedHere = true;
 	}
+	// Free memory
+	if (loop > 0) {
+		PetscCallVoid(PetscOptionsDestroy(&petscOptions));
+		PetscCallVoid(VecDestroy(&C));
+		PetscCallVoid(TSDestroy(&ts));
+		PetscCallVoid(DMDestroy(&da));
+	}
 
 	/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 	 Create the solver options
@@ -358,7 +365,9 @@ PetscSolver::solve()
 	while (reason == TS_CONVERGED_USER) {
 		// The interface already initialized the first loop
 		if (loopNumber > 0) {
+			PetscCallVoid(PetscOptionsPop());
 			initialize(loopNumber, time, oldDA, oldC);
+			PetscCallVoid(PetscOptionsPush(petscOptions));
 		}
 
 		/*
diff --git a/xolotl/solver/src/monitor/PetscMonitor1D.cpp b/xolotl/solver/src/monitor/PetscMonitor1D.cpp
index 13fb9785..fa5a86a0 100644
--- a/xolotl/solver/src/monitor/PetscMonitor1D.cpp
+++ b/xolotl/solver/src/monitor/PetscMonitor1D.cpp
@@ -1951,6 +1951,9 @@ PetscMonitor1D::postEventFunction(TS ts, PetscInt nevents, PetscInt eventList[],
 			if (nGridPoints > 0) {
 				_solverHandler->setSurfaceOffset(nGridPoints);
 				PetscCall(TSSetConvergedReason(ts, TS_CONVERGED_USER));
+
+				// Restore the solutionArray
+				PetscCall(DMDAVecRestoreArrayDOF(da, solution, &solutionArray));
 				PetscFunctionReturn(0);
 			}
 		}
diff --git a/xolotl/util/include/xolotl/util/Atomics.h b/xolotl/util/include/xolotl/util/Atomics.h
index 21bb5e8a..eb6e69f6 100644
--- a/xolotl/util/include/xolotl/util/Atomics.h
+++ b/xolotl/util/include/xolotl/util/Atomics.h
@@ -11,7 +11,7 @@ KOKKOS_INLINE_FUNCTION
 bool
 atomicCompareExchangeStrong(T* ptr, T expected, T desired)
 {
-    return expected == Kokkos::atomic_compare_exchange(ptr, expected, desired);
-}
-}
+	return expected == Kokkos::atomic_compare_exchange(ptr, expected, desired);
 }
+} // namespace util
+} // namespace xolotl