Merge branch 'pgrete/bump-parth-for-rr' into pgrete/next-w-tracer-latest

parthenon-hpc-lab · Jul 18, 2024 · 73e59e9 · 73e59e9
2 parents bae0ce0 + 3a8fe16
commit 73e59e9
Show file tree

Hide file tree

Showing 9 changed files with 23 additions and 15 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,11 +10,17 @@
 ### Fixed (not changing behavior/API/variables/...)
 
 ### Infrastructure
+- [[PR 109]](https://github.com/parthenon-hpc-lab/athenapk/pull/109) Bump Parthenon to latest develop (2024-05-29)
+- [[PR 105]](https://github.com/parthenon-hpc-lab/athenapk/pull/105) Bump Parthenon to latest develop (2024-03-13)
 - [[PR 84]](https://github.com/parthenon-hpc-lab/athenapk/pull/84) Added `CHANGELOG.md`
 
 ### Removed (removing behavior/API/varaibles/...)
 
 ### Incompatibilities (i.e. breaking changes)
+- [[PR 109]](https://github.com/parthenon-hpc-lab/athenapk/pull/109) Bump Parthenon to latest develop (2024-05-29)
+  - Changed signature of `UserWorkBeforeOutput` to include `SimTime` as last paramter
+  - Fixes bitwise idential restarts for AMR simulations (the derefinement counter is now included)
+  - Order of operations in flux-correction has changed (expect round-off error differences to previous results for AMR sims)
 - [[PR 84]](https://github.com/parthenon-hpc-lab/athenapk/pull/84) Bump Parthenon to latest develop (2024-02-15)
   - Updated access to block dimension: `pmb->block_size.nx1` -> `pmb->block_size.nx(X1DIR)` (and similarly x2 and x3)
   - Update access to mesh size: `pmesh->mesh_size.x1max` -> `pmesh->mesh_size.xmax(X1DIR)` (and similarly x2, x3, and min)

diff --git a/docs/cluster.md b/docs/cluster.md
@@ -534,7 +534,7 @@ fixed_mass_rate = 1.0
 
 ## SNIA Feedback
 
-Following [Prasad 2020](doi.org/10.1093/mnras/112.2.195), AthenaPK can inject
+Following [Prasad 2020](https://doi.org/10.3847/1538-4357/abc33c), AthenaPK can inject
 mass and energy from type Ia supernovae following the mass profile of the BCG.
 This SNIA feedback can be configured with
 ```

diff --git a/external/parthenon b/external/parthenon
diff --git a/src/hydro/hydro_driver.cpp b/src/hydro/hydro_driver.cpp
@@ -717,7 +717,7 @@ TaskCollection HydroDriver::MakeTaskCollection(BlockList_t &blocks, int stage) {
     {
       for (auto &pmb : blocks) {
         auto &tl = sync_region_tr[0];
-        auto &sd = pmb->swarm_data.Get();
+        auto &sd = pmb->meshblock_data.Get()->GetSwarmData();
         auto reset_comms =
             tl.AddTask(none, &SwarmContainer::ResetCommunication, sd.get());
       }
@@ -727,7 +727,7 @@ TaskCollection HydroDriver::MakeTaskCollection(BlockList_t &blocks, int stage) {
     for (int n = 0; n < blocks.size(); n++) {
       auto &tl = async_region_tr[n];
       auto &pmb = blocks[n];
-      auto &sd = pmb->swarm_data.Get();
+      auto &sd = pmb->meshblock_data.Get()->GetSwarmData();
       auto &mbd0 = pmb->meshblock_data.Get("base");
       auto tracer_advect =
           tl.AddTask(none, Tracers::AdvectTracers, mbd0.get(), integrator->dt);

diff --git a/src/pgen/cloud.cpp b/src/pgen/cloud.cpp
@@ -229,9 +229,10 @@ void InflowWindX2(std::shared_ptr<MeshBlockData<Real>> &mbd, bool coarse) {
   const auto Bx_ = Bx;
   const auto By_ = By;
   const auto Bz_ = Bz;
+  const bool fine = false;
   pmb->par_for_bndry(
       "InflowWindX2", nb, IndexDomain::inner_x2, parthenon::TopologicalElement::CC,
-      coarse, KOKKOS_LAMBDA(const int, const int &k, const int &j, const int &i) {
+      coarse, fine, KOKKOS_LAMBDA(const int, const int &k, const int &j, const int &i) {
         cons(IDN, k, j, i) = rho_wind_;
         cons(IM2, k, j, i) = mom_wind_;
         cons(IEN, k, j, i) = rhoe_wind_ + 0.5 * mom_wind_ * mom_wind_ / rho_wind_;

diff --git a/src/pgen/cluster.cpp b/src/pgen/cluster.cpp
@@ -812,7 +812,8 @@ void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md) {
   }
 }
 
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) {
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime & /*tm*/) {
   // get hydro
   auto pkg = pmb->packages.Get("Hydro");
   const Real gam = pin->GetReal("hydro", "gamma");

diff --git a/src/pgen/pgen.hpp b/src/pgen/pgen.hpp
@@ -100,7 +100,8 @@ using namespace parthenon::driver::prelude;
 void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg);
 void InitUserMeshData(ParameterInput *pin);
 void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md);
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin);
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime &tm);
 void ClusterUnsplitSrcTerm(MeshData<Real> *md, const parthenon::SimTime &tm,
                            const Real beta_dt);
 void ClusterSplitSrcTerm(MeshData<Real> *md, const parthenon::SimTime &tm,
@@ -121,7 +122,8 @@ void ProblemGenerator(Mesh *pm, parthenon::ParameterInput *pin, MeshData<Real> *
 void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg);
 void Driving(MeshData<Real> *md, const parthenon::SimTime &tm, const Real dt);
 void SetPhases(MeshBlock *pmb, ParameterInput *pin);
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin);
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime &tm);
 void Cleanup();
 } // namespace turbulence
 

diff --git a/src/pgen/turbulence.cpp b/src/pgen/turbulence.cpp
@@ -440,8 +440,7 @@ void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md) {
 
     for (int b = 0; b < md->NumBlocks(); b++) {
       pmb = md->GetBlockData(b)->GetBlockPointer();
-      auto &sd = pmb->swarm_data.Get();
-      auto &swarm = pmb->swarm_data.Get()->Get("tracers");
+      auto &swarm = pmb->meshblock_data.Get()->GetSwarmData()->Get("tracers");
       auto rng_pool = tracer_pkg->Param<RNGPool>("rng_pool");
 
       const Real &x_min = pmb->coords.Xf<1>(ib.s);
@@ -814,7 +813,8 @@ void Driving(MeshData<Real> *md, const parthenon::SimTime &tm, const Real dt) {
   InjectBlob(md, tm, dt);
 }
 
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) {
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime & /*tm*/) {
   auto hydro_pkg = pmb->packages.Get("Hydro");
 
   // Store (common) acceleration field in spectral space

diff --git a/src/tracers/tracers.cpp b/src/tracers/tracers.cpp
@@ -112,8 +112,7 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
 
 TaskStatus AdvectTracers(MeshBlockData<Real> *mbd, const Real dt) {
   auto *pmb = mbd->GetParentPointer();
-  auto &sd = pmb->swarm_data.Get();
-  auto &swarm = sd->Get("tracers");
+  auto &swarm = pmb->meshblock_data.Get()->GetSwarmData()->Get("tracers");
 
   auto &x = swarm->Get<Real>("x").Get();
   auto &y = swarm->Get<Real>("y").Get();
@@ -207,8 +206,7 @@ TaskStatus FillTracers(MeshData<Real> *md, parthenon::SimTime &tm) {
   const auto &prim_pack = md->PackVariables(std::vector<std::string>{"prim"});
   for (int b = 0; b < md->NumBlocks(); b++) {
     auto *pmb = md->GetBlockData(b)->GetBlockPointer();
-    auto &sd = pmb->swarm_data.Get();
-    auto &swarm = sd->Get("tracers");
+    auto &swarm = pmb->meshblock_data.Get()->GetSwarmData()->Get("tracers");
 
     // TODO(pgrete) cleanup once get swarm packs (currently in development upstream)
     // pull swarm vars