From 513e36275ded3a386c742c293cdf328b421ca57b Mon Sep 17 00:00:00 2001 From: Ben Wibking Date: Wed, 13 Mar 2024 09:03:16 -0400 Subject: [PATCH 1/6] update parthenon to 314ac5c (#105) * update parthenon to 314ac5c * Update CHANGELOG.md --------- Co-authored-by: Philipp Grete --- CHANGELOG.md | 1 + external/parthenon | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73a31d4b..83bc715d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ ### Fixed (not changing behavior/API/variables/...) ### Infrastructure +- [[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/...) diff --git a/external/parthenon b/external/parthenon index 88ece809..314ac5c0 160000 --- a/external/parthenon +++ b/external/parthenon @@ -1 +1 @@ -Subproject commit 88ece809dc56ae16d695db8d9051433bff01feb1 +Subproject commit 314ac5c03178748c17161ce691ef24d535f0b539 From d8f0a553752805f46702cd7f0620a22614074821 Mon Sep 17 00:00:00 2001 From: Ben Wibking Date: Sun, 17 Mar 2024 20:23:07 -0400 Subject: [PATCH 2/6] update parthenon to fix restarts --- external/parthenon | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external/parthenon b/external/parthenon index 314ac5c0..a66670bb 160000 --- a/external/parthenon +++ b/external/parthenon @@ -1 +1 @@ -Subproject commit 314ac5c03178748c17161ce691ef24d535f0b539 +Subproject commit a66670bbc767fe03ef48a33794c6cd288ee517ed From 567b2b94c2c118bf8eb462b46ce38a7b46034114 Mon Sep 17 00:00:00 2001 From: Philipp Grete Date: Wed, 29 May 2024 15:46:14 +0200 Subject: [PATCH 3/6] bump Parthenon --- CHANGELOG.md | 5 +++++ external/parthenon | 2 +- src/pgen/cluster.cpp | 3 ++- src/pgen/pgen.hpp | 6 ++++-- src/pgen/turbulence.cpp | 3 ++- 5 files changed, 14 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 83bc715d..48ebc38a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,12 +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/external/parthenon b/external/parthenon index a66670bb..616eab2e 160000 --- a/external/parthenon +++ b/external/parthenon @@ -1 +1 @@ -Subproject commit a66670bbc767fe03ef48a33794c6cd288ee517ed +Subproject commit 616eab2e785fce6afa72a1e0023cf3f856d1fe6f diff --git a/src/pgen/cluster.cpp b/src/pgen/cluster.cpp index 1e73d8b5..ecc19336 100644 --- a/src/pgen/cluster.cpp +++ b/src/pgen/cluster.cpp @@ -812,7 +812,8 @@ void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData *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 index 182d8497..b3e55aad 100644 --- a/src/pgen/pgen.hpp +++ b/src/pgen/pgen.hpp @@ -99,7 +99,8 @@ using namespace parthenon::driver::prelude; void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg); void InitUserMeshData(ParameterInput *pin); void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData *md); -void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin); +void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin, + const parthenon::SimTime &tm); void ClusterUnsplitSrcTerm(MeshData *md, const parthenon::SimTime &tm, const Real beta_dt); void ClusterSplitSrcTerm(MeshData *md, const parthenon::SimTime &tm, @@ -120,7 +121,8 @@ void ProblemGenerator(Mesh *pm, parthenon::ParameterInput *pin, MeshData * void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg); void Driving(MeshData *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 index 2c9ff9a7..b137a9ad 100644 --- a/src/pgen/turbulence.cpp +++ b/src/pgen/turbulence.cpp @@ -450,7 +450,8 @@ void Driving(MeshData *md, const parthenon::SimTime &tm, const Real dt) { Perturb(md, 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 From a40bb0f3daf16e3888944ca7afad90edb686446f Mon Sep 17 00:00:00 2001 From: Philipp Grete Date: Fri, 7 Jun 2024 15:00:44 +0200 Subject: [PATCH 4/6] Fix link to reference in doc --- docs/cluster.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/cluster.md b/docs/cluster.md index 9e3eaaac..11864b6c 100644 --- 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 ``` From e778d03106eb26dfb21847afbc2163f63fa28fba Mon Sep 17 00:00:00 2001 From: Philipp Grete Date: Wed, 12 Jun 2024 10:06:50 +0200 Subject: [PATCH 5/6] Bump Parth to include restart ghost fix --- external/parthenon | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/external/parthenon b/external/parthenon index 616eab2e..7d5dbfaa 160000 --- a/external/parthenon +++ b/external/parthenon @@ -1 +1 @@ -Subproject commit 616eab2e785fce6afa72a1e0023cf3f856d1fe6f +Subproject commit 7d5dbfaa7403fe95b3b36b550ae5e6b743c3f711 From 3a8fe16751462fe1dbd440429e9ecbc3d993cb48 Mon Sep 17 00:00:00 2001 From: Ben Wibking Date: Tue, 18 Jun 2024 15:19:22 -0400 Subject: [PATCH 6/6] update parthenon to openpmd branch --- external/parthenon | 2 +- src/pgen/cloud.cpp | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/external/parthenon b/external/parthenon index 7d5dbfaa..a44da269 160000 --- a/external/parthenon +++ b/external/parthenon @@ -1 +1 @@ -Subproject commit 7d5dbfaa7403fe95b3b36b550ae5e6b743c3f711 +Subproject commit a44da26921b7db024a104ed3f18dd59c35ec57a5 diff --git a/src/pgen/cloud.cpp b/src/pgen/cloud.cpp index b496dd2d..9ea3f5fb 100644 --- a/src/pgen/cloud.cpp +++ b/src/pgen/cloud.cpp @@ -222,9 +222,10 @@ void InflowWindX2(std::shared_ptr> &mbd, bool coarse) { const auto rhoe_wind_ = rhoe_wind; const auto Bx_ = Bx; const auto By_ = By; + 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_;