New particle interface using derived classes #827

chongchonghe · 2024-12-19T14:45:55Z

Description

The physics particle interface provides a flexible and extensible system for managing different types of particles in the simulation. It uses a combination of the Strategy pattern and Registry pattern to handle multiple particle types through a common interface.

Core Components

1. PhysicsParticleDescriptor (Base Class)

class PhysicsParticleDescriptor {
		protected:
  int massIndex_{-1};	// index for gravity mass, -1 if not used
  int lumIndex_{-1};	// index for radiation luminosity, -1 if not used
  int birthTimeIndex_{-1}; // index for birth time, -1 if not used
  bool interactsWithHydro_{false}; // whether particles interact with hydro

		public:
	virtual void redistribute(int lev) = 0;
  virtual void writePlotFile(...) = 0;
  virtual void depositRadiation(...) = 0;
  virtual void depositMass(...) = 0;
  // ...
};

This abstract base class defines the interface that all particle descriptors must implement. It provides virtual methods for common particle operations like:

Redistribution across processors
Writing to plot files and checkpoints
Depositing radiation and mass to the grid

2. Concrete Descriptor Classes

Currently, the system provides three specialized descriptor classes. More can be added by subclassing PhysicsParticleDescriptor.

RadParticleDescriptor: For radiation-emitting particles
CICParticleDescriptor: For Cloud-In-Cell (gravitating) particles
CICRadParticleDescriptor: For particles that both emit radiation and interact via CIC

3. PhysicsParticleRegister

template <typename problem_t>
class PhysicsParticleRegister {
    void registerParticleType(const std::string &name, 
                            std::unique_ptr<ParticleDescriptor> descriptor);
    void depositRadiation(...);
    void depositMass(...);
    // ...
};

A registry that manages all particle descriptors and provides high-level operations that apply to all registered particles.

Usage

1. Creating and Registering Particles

See example in src/simulation.hpp: InitParticles()

// Create particle descriptor
auto radParticleDesc = std::make_unique<RadParticleDescriptor<problem_t>>(
    -1,                // mass index
    RadParticleLumIdx, // luminosity index 
    RadParticleBirthTimeIdx, // birth time index
    false              // hydro interaction flag
);

// Create particle container
RadParticles = std::make_unique<RadParticleContainer<problem_t>>(this);

// Set container in descriptor
radParticleDesc->setParticleContainer(RadParticles.get());

// Register with particle register
particleRegister_->registerParticleType("Rad_particles", std::move(radParticleDesc));

2. Using the Interface

Once particles are registered, you can perform operations on all particles through the register:

// Deposit radiation from all particles that have luminosity
particleRegister_->depositRadiation(radEnergySource, lev, current_time);

// Redistribute particles after grid changes
particleRegister_->redistribute(lev);

// Write particle data to plot files
particleRegister_->writePlotFile(plotfilename);

Key Features

Type Safety: Each descriptor handles type-safe casting of its particle container internally.
Extensibility: New particle types can be added by:
- Creating a new particle container class
- Creating a new descriptor class that inherits from PhysicsParticleDescriptor
- Implementing the required virtual methods
Unified Interface: All particle operations can be performed through the register without knowing the specific particle types.

Selective Operations: The system automatically handles operations only for particles that support them:

// Only particles with luminosity will deposit radiation
if (descriptor->getLumIndex() >= 0) {
    descriptor->depositRadiation(...);
}

Adding a New Particle Type

Create a new particle container and iterator:

using XXXParticleContainer = amrex::AmrParticleContainer<XXXParticleRealComps>;
using XXXParticleIterator = amrex::ParIter<XXXParticleRealComps>;

Create a new descriptor class:

class XXXParticleDescriptor : public PhysicsParticleDescriptor {
    void redistribute(int lev) override {
        if (auto *container = dynamic_cast<XXXParticleContainer*>(
            this->neighborParticleContainer_)) {
            container->Redistribute(lev);
        }
    }
    // Implement other virtual methods
};

Define a unique_ptr to the new particle container in AMRSimulation:

std::unique_ptr<XXXParticleContainer> XXXParticles;

Register the new particle type in AMRSimulation::InitPhyParticles():

auto newParticleDesc = std::make_unique<XXXParticleDescriptor>(...);
...
particleRegister_->registerParticleType("XXX_particles", std::move(newParticleDesc));
// Initialize particles through derived class
createInitialXXXParticles();

Register the new particle type in AMRSimulation::ReadCheckpointFile():

particleRegister_->registerParticleType("XXX_particles", std::move(newParticleDesc));

New test problems

This implementation is totally working, passing both RadParticle and GravRadParticle3D tests.

Related issues

None.

Checklist

Before this pull request can be reviewed, all of these tasks should be completed. Denote completed tasks with an x inside the square brackets [ ] in the Markdown source below:

I have added a description (see above).
I have added a link to any related issues (if applicable; see above).
I have read the Contributing Guide.
I have added tests for any new physics that this PR adds to the code.
(For quokka-astro org members) I have manually triggered the GPU tests with the magic comment /azp run.

so that SetRadEnergySource is called on all Fabs at a level

…assing tests

for more information, see https://pre-commit.ci

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 68. Check the log or trigger a new build to see more.

src/particles/PhysicsParticles.hpp

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

for more information, see https://pre-commit.ci

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 70. Check the log or trigger a new build to see more.

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+
+const double lum1 = 1.0;
+
+template <> struct quokka::EOS_Traits<ParticleProblem> {


warning: no header providing "quokka::EOS_Traits" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "test_grav_rad_particle_3D.hpp" + #include "hydro/EOS.hpp" + #include "test_grav_rad_particle_3D.hpp"

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	static constexpr double gamma = 5. / 3.;
+};
+
+template <> struct Physics_Traits<ParticleProblem> {


warning: no header providing "Physics_Traits" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "test_grav_rad_particle_3D.hpp" + #include "physics_info.hpp" + #include "test_grav_rad_particle_3D.hpp"

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	CICRadParticles->InitFromAsciiFile("GravRadParticles3D.txt", nreal_extra, nullptr);
+}
+
+template <> AMREX_GPU_HOST_DEVICE auto RadSystem<ParticleProblem>::ComputePlanckOpacity(const double /*rho*/, const double /*Tgas*/) -> amrex::Real


warning: no header providing "AMREX_GPU_HOST_DEVICE" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_GpuQualifiers.H" + #include "AMReX_Vector.H"

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	return kappa0;
+}
+
+template <> void QuokkaSimulation<ParticleProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)


warning: no header providing "quokka::grid" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "test_grav_rad_particle_3D.hpp" + #include "grid.hpp" + #include "test_grav_rad_particle_3D.hpp"

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+template <> void QuokkaSimulation<ParticleProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
+{
+	const amrex::Box &indexRange = grid_elem.indexRange_;
+	const amrex::Array4<double> &state_cc = grid_elem.array_;


warning: no header providing "amrex::Array4" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:7:

- #include "AMReX_BCRec.H" + #include "AMReX_Array4.H" + #include "AMReX_BCRec.H"

github-actions · 2024-12-23T08:20:49Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	const auto Egas0 = initial_Egas;
+
+	// loop over the grid and set the initial condition
+	amrex::ParallelFor(indexRange, [=] AMREX_GPU_DEVICE(int i, int j, int k) {


warning: no header providing "amrex::ParallelFor" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_GpuLaunchFunctsC.H" + #include "AMReX_Vector.H"

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 64. Check the log or trigger a new build to see more.

src/particles/PhysicsParticles.hpp

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

github-actions · 2024-12-30T00:38:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+
+	// get particle positions
+	quokka::CICRadParticleContainer<ParticleProblem> analysisPC{};
+	amrex::Box const box(amrex::IntVect{AMREX_D_DECL(0, 0, 0)}, amrex::IntVect{AMREX_D_DECL(1, 1, 1)});


warning: no header providing "AMREX_D_DECL" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_SPACE.H" + #include "AMReX_Vector.H"

github-actions · 2024-12-30T00:38:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	quokka::CICRadParticleContainer<ParticleProblem> analysisPC{};
+	amrex::Box const box(amrex::IntVect{AMREX_D_DECL(0, 0, 0)}, amrex::IntVect{AMREX_D_DECL(1, 1, 1)});
+	amrex::Geometry const geom(box);
+	amrex::BoxArray const boxArray(box);


warning: no header providing "amrex::BoxArray" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_BoxArray.H" + #include "AMReX_Vector.H"

github-actions · 2024-12-30T00:38:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	amrex::Geometry const geom(box);
+	amrex::BoxArray const boxArray(box);
+	amrex::Vector<int> const ranks({0}); // workaround nvcc bug
+	amrex::DistributionMapping const dmap(ranks);


warning: no header providing "amrex::DistributionMapping" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_DistributionMapping.H" + #include "AMReX_Vector.H"

github-actions · 2024-12-30T00:38:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	    sim.particleRegister_.getParticleDescriptor("CICRad_particles")->getParticleContainer<quokka::CICRadParticleContainer<ParticleProblem>>();
+	analysisPC.copyParticles(*container);
+
+	if (amrex::ParallelDescriptor::IOProcessor()) {


warning: no header providing "amrex::ParallelDescriptor::IOProcessor" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:10:

- #include "AMReX_Vector.H" + #include "AMReX_ParallelDescriptor.H" + #include "AMReX_Vector.H"

github-actions · 2024-12-30T00:38:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	analysisPC.copyParticles(*container);
+
+	if (amrex::ParallelDescriptor::IOProcessor()) {
+		quokka::CICRadParticleIterator<ParticleProblem> const pIter(analysisPC, 0);


warning: no header providing "quokka::CICRadParticleIterator" is directly included [misc-include-cleaner]

quokka::CICRadParticleIterator<ParticleProblem> const pIter(analysisPC, 0); ^

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 63. Check the log or trigger a new build to see more.

src/particles/PhysicsParticles.hpp

github-actions · 2024-12-30T01:02:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+
+#include "AMReX.H"
+#include "AMReX_BCRec.H"
+#include "AMReX_BC_TYPES.H"


warning: included header AMReX_BCRec.H is not used directly [misc-include-cleaner]

Suggested change

#include "AMReX_BC_TYPES.H"

#include "AMReX_BC_TYPES.H"

github-actions · 2024-12-30T01:02:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+#include "AMReX_BC_TYPES.H"
+#include "AMReX_Box.H"
+#include "AMReX_GpuLaunchFunctsC.H"
+#include "AMReX_REAL.H"


warning: included header AMReX_GpuLaunchFunctsC.H is not used directly [misc-include-cleaner]

Suggested change

#include "AMReX_REAL.H"

#include "AMReX_REAL.H"

github-actions · 2024-12-30T01:02:10Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+#include "AMReX_Box.H"
+#include "AMReX_GpuLaunchFunctsC.H"
+#include "AMReX_REAL.H"
+#include "AMReX_Vector.H"


warning: included header AMReX_REAL.H is not used directly [misc-include-cleaner]

Suggested change

#include "AMReX_Vector.H"

#include "AMReX_Vector.H"

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+#include "AMReX_GpuLaunchFunctsC.H"
+#include "AMReX_REAL.H"
+#include "AMReX_Vector.H"
+#include "QuokkaSimulation.hpp"


warning: included header AMReX_Vector.H is not used directly [misc-include-cleaner]

Suggested change

#include "QuokkaSimulation.hpp"

#include "QuokkaSimulation.hpp"

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+#include "QuokkaSimulation.hpp"
+#include "hydro/EOS.hpp"
+#include "particles/PhysicsParticles.hpp"
+#include "radiation/radiation_system.hpp"


warning: included header PhysicsParticles.hpp is not used directly [misc-include-cleaner]

Suggested change

#include "radiation/radiation_system.hpp"

#include "radiation/radiation_system.hpp"

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	static constexpr double gamma = 5. / 3.;
+};
+
+template <> struct Physics_Traits<ParticleProblem> {


warning: no header providing "Physics_Traits" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:18:

- #include "radiation/radiation_system.hpp" + #include "physics_info.hpp" + #include "radiation/radiation_system.hpp"

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	CICRadParticles->InitFromAsciiFile("GravRadParticles3D.txt", nreal_extra, nullptr);
+}
+
+template <> AMREX_GPU_HOST_DEVICE auto RadSystem<ParticleProblem>::ComputePlanckOpacity(const double /*rho*/, const double /*Tgas*/) -> amrex::Real


warning: no header providing "AMREX_GPU_HOST_DEVICE" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:13:

- #include "AMReX_REAL.H" + #include "AMReX_GpuQualifiers.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	};
+
+	// Boundary conditions
+	constexpr int nvars = RadSystem<ParticleProblem>::nvar_;


warning: variable 'nvars' is not initialized [cppcoreguidelines-init-variables]

Suggested change

constexpr int nvars = RadSystem<ParticleProblem>::nvar_;

constexpr int nvars = 0 = RadSystem<ParticleProblem>::nvar_;

github-actions · 2024-12-30T01:02:11Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	sim.evolve();
+
+	// compute total radiation energy
+	const double total_Erad_over_vol = sim.state_new_cc_[0].sum(RadSystem<ParticleProblem>::radEnergy_index);


warning: variable 'total_Erad_over_vol' is not initialized [cppcoreguidelines-init-variables]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:20:

+ + #include <math.h>

Suggested change

const double total_Erad_over_vol = sim.state_new_cc_[0].sum(RadSystem<ParticleProblem>::radEnergy_index);

const double total_Erad_over_vol = NAN = sim.state_new_cc_[0].sum(RadSystem<ParticleProblem>::radEnergy_index);

for more information, see https://pre-commit.ci

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 58. Check the log or trigger a new build to see more.

src/particles/PhysicsParticles.hpp

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	static constexpr double gamma = 5. / 3.;
+};
+
+template <> struct Physics_Traits<ParticleProblem> {


warning: no header providing "Physics_Traits" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:17:

- #include "radiation/radiation_system.hpp" + #include "physics_info.hpp" + #include "radiation/radiation_system.hpp"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	CICRadParticles->InitFromAsciiFile("GravRadParticles3D.txt", nreal_extra, nullptr);
+}
+
+template <> AMREX_GPU_HOST_DEVICE auto RadSystem<ParticleProblem>::ComputePlanckOpacity(const double /*rho*/, const double /*Tgas*/) -> amrex::Real


warning: no header providing "AMREX_GPU_HOST_DEVICE" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_GpuQualifiers.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	return kappa0;
+}
+
+template <> void QuokkaSimulation<ParticleProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)


warning: no header providing "quokka::grid" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:15:

- #include "hydro/EOS.hpp" + #include "grid.hpp" + #include "hydro/EOS.hpp"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+template <> void QuokkaSimulation<ParticleProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
+{
+	const amrex::Box &indexRange = grid_elem.indexRange_;
+	const amrex::Array4<double> &state_cc = grid_elem.array_;


warning: no header providing "amrex::Array4" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:9:

- #include "AMReX_BCRec.H" + #include "AMReX_Array4.H" + #include "AMReX_BCRec.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	const auto Egas0 = initial_Egas;
+
+	// loop over the grid and set the initial condition
+	amrex::ParallelFor(indexRange, [=] AMREX_GPU_DEVICE(int i, int j, int k) {


warning: no header providing "amrex::ParallelFor" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_GpuLaunchFunctsC.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+
+	// get particle positions
+	quokka::CICRadParticleContainer<ParticleProblem> analysisPC{};
+	amrex::Box const box(amrex::IntVect{AMREX_D_DECL(0, 0, 0)}, amrex::IntVect{AMREX_D_DECL(1, 1, 1)});


warning: no header providing "AMREX_D_DECL" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:13:

- #include "AMReX_Vector.H" + #include "AMReX_SPACE.H" + #include "AMReX_Vector.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	quokka::CICRadParticleContainer<ParticleProblem> analysisPC{};
+	amrex::Box const box(amrex::IntVect{AMREX_D_DECL(0, 0, 0)}, amrex::IntVect{AMREX_D_DECL(1, 1, 1)});
+	amrex::Geometry const geom(box);
+	amrex::BoxArray const boxArray(box);


warning: no header providing "amrex::BoxArray" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_BoxArray.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	amrex::Geometry const geom(box);
+	amrex::BoxArray const boxArray(box);
+	amrex::Vector<int> const ranks({0}); // workaround nvcc bug
+	amrex::DistributionMapping const dmap(ranks);


warning: no header providing "amrex::DistributionMapping" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_DistributionMapping.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-30T12:54:24Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	    sim.particleRegister_.getParticleDescriptor("CICRad_particles")->getParticleContainer<quokka::CICRadParticleContainer<ParticleProblem>>();
+	analysisPC.copyParticles(*container);
+
+	if (amrex::ParallelDescriptor::IOProcessor()) {


warning: no header providing "amrex::ParallelDescriptor::IOProcessor" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_ParallelDescriptor.H" + #include "AMReX_REAL.H"

chongchonghe · 2024-12-31T04:36:30Z

/azp run

azure-pipelines · 2024-12-31T04:36:45Z

Azure Pipelines successfully started running 2 pipeline(s).

chongchonghe · 2024-12-31T06:17:34Z

/azp run

azure-pipelines · 2024-12-31T06:17:50Z

Azure Pipelines successfully started running 2 pipeline(s).

azure-pipelines · 2024-12-31T06:24:15Z

Azure Pipelines successfully started running 2 pipeline(s).

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 49. Check the log or trigger a new build to see more.

src/particles/PhysicsParticles.hpp

github-actions · 2024-12-31T06:36:57Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+	if (amrex::ParallelDescriptor::IOProcessor()) {
+		quokka::CICRadParticleIterator<ParticleProblem> const pIter(analysisPC, 0);
+		if (pIter.isValid()) {
+			const amrex::Long np = pIter.numParticles();


warning: no header providing "amrex::Long" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_INT.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-31T06:36:57Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+			// copy particles from device to host
+			quokka::CICRadParticleContainer<ParticleProblem>::ParticleType *pData = particles().data();
+			amrex::Vector<quokka::CICRadParticleContainer<ParticleProblem>::ParticleType> pData_h(np);
+			amrex::Gpu::copy(amrex::Gpu::deviceToHost, pData, pData + np,


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

amrex::Gpu::copy(amrex::Gpu::deviceToHost, pData, pData + np, ^

github-actions · 2024-12-31T06:36:57Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+			// copy particles from device to host
+			quokka::CICRadParticleContainer<ParticleProblem>::ParticleType *pData = particles().data();
+			amrex::Vector<quokka::CICRadParticleContainer<ParticleProblem>::ParticleType> pData_h(np);
+			amrex::Gpu::copy(amrex::Gpu::deviceToHost, pData, pData + np,


warning: no header providing "amrex::Gpu::copy" is directly included [misc-include-cleaner]

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp:12:

- #include "AMReX_REAL.H" + #include "AMReX_GpuContainers.H" + #include "AMReX_REAL.H"

github-actions · 2024-12-31T06:36:57Z

src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp

+			// copy particles from device to host
+			quokka::CICRadParticleContainer<ParticleProblem>::ParticleType *pData = particles().data();
+			amrex::Vector<quokka::CICRadParticleContainer<ParticleProblem>::ParticleType> pData_h(np);
+			amrex::Gpu::copy(amrex::Gpu::deviceToHost, pData, pData + np,


warning: no header providing "amrex::Gpu::deviceToHost" is directly included [misc-include-cleaner]

amrex::Gpu::copy(amrex::Gpu::deviceToHost, pData, pData + np, ^

github-actions · 2024-12-31T06:36:57Z

src/problems/RadParticle/test_radparticle.cpp

+	static constexpr int beta_order = 0;
+	static constexpr OpacityModel opacity_model = OpacityModel::piecewise_constant_opacity;
+	static constexpr double energy_unit = 1.0;
+	static constexpr amrex::GpuArray<double, nGroups_ + 1> radBoundaries{0.001, 1.0, 3.0, 100.0};


warning: no header providing "amrex::GpuArray" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:6:

- #include "AMReX_Array4.H" + #include "AMReX_Array.H" + #include "AMReX_Array4.H"

github-actions · 2024-12-31T06:36:58Z

src/problems/RadParticle/test_radparticle.cpp

+// }
+
+template <>
+AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto


warning: no header providing "AMREX_FORCE_INLINE" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:8:

- #include "AMReX_GpuQualifiers.H" + #include "AMReX_Extension.H" + #include "AMReX_GpuQualifiers.H"

github-actions · 2024-12-31T06:36:58Z

src/problems/RadParticle/test_radparticle.cpp

+	const auto Egas0 = initial_Egas;
+
+	// loop over the grid and set the initial condition
+	amrex::ParallelFor(indexRange, [=] AMREX_GPU_DEVICE(int i, int j, int k) {


warning: no header providing "amrex::ParallelFor" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:8:

- #include "AMReX_GpuQualifiers.H" + #include "AMReX_GpuLaunchFunctsC.H" + #include "AMReX_GpuQualifiers.H"

github-actions · 2024-12-31T06:36:58Z

src/problems/RadParticle/test_radparticle.cpp

+	// loop over the grid and set the initial condition
+	amrex::ParallelFor(indexRange, [=] AMREX_GPU_DEVICE(int i, int j, int k) {
+		for (int g = 0; g < nGroups_; ++g) {
+			state_cc(i, j, k, RadSystem<ParticleProblem>::radEnergy_index + Physics_NumVars::numRadVars * g) = Erad0;


warning: no header providing "Physics_NumVars" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:13:

- #include "radiation/radiation_system.hpp" + #include "physics_numVars.hpp" + #include "radiation/radiation_system.hpp"

github-actions · 2024-12-31T06:36:58Z

src/problems/RadParticle/test_radparticle.cpp

+
+	// Boundary conditions
+	constexpr int nvars = RadSystem<ParticleProblem>::nvar_;
+	amrex::Vector<amrex::BCRec> BCs_cc(nvars);


warning: no header providing "amrex::BCRec" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:7:

- #include "AMReX_Box.H" + #include "AMReX_BCRec.H" + #include "AMReX_Box.H"

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 29. Check the log or trigger a new build to see more.

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+
+	// Boundary conditions
+	constexpr int nvars = RadSystem<ParticleProblem>::nvar_;
+	amrex::Vector<amrex::BCRec> BCs_cc(nvars);


warning: no header providing "amrex::Vector" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:9:

- #include "QuokkaSimulation.hpp" + #include "AMReX_Vector.H" + #include "QuokkaSimulation.hpp"

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+	amrex::Vector<amrex::BCRec> BCs_cc(nvars);
+	for (int n = 0; n < nvars; ++n) {
+		for (int i = 0; i < AMREX_SPACEDIM; ++i) {
+			BCs_cc[n].setLo(i, amrex::BCType::int_dir); // periodic


warning: no header providing "amrex::BCType::int_dir" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:7:

- #include "AMReX_Box.H" + #include "AMReX_BC_TYPES.H" + #include "AMReX_Box.H"

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+	const double dx = sim.Geom(0).CellSize(0);
+
+	// compute error norm
+	std::vector<double> Erad_group0(nx);


warning: no header providing "std::vector" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:16:

- #ifdef HAVE_PYTHON + #include <vector> + #ifdef HAVE_PYTHON

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+	double tot_lum_group1 = 0.0;
+	double tot_lum_group2 = 0.0;
+	for (int i = 0; i < nx; ++i) {
+		amrex::Real const x = position[i];


warning: no header providing "amrex::Real" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:9:

- #include "QuokkaSimulation.hpp" + #include "AMReX_REAL.H" + #include "QuokkaSimulation.hpp"

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+	const double lum_exact_group2 = lum3 * tmax;
+
+	const double err_norm =
+	    std::abs(tot_lum_group0 - lum_exact_group0) + std::abs(tot_lum_group1 - lum_exact_group1) + std::abs(tot_lum_group2 - lum_exact_group2);


warning: no header providing "std::abs" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:15:

- #include <fmt/format.h> + #include <cstdlib> + #include <fmt/format.h>

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle/test_radparticle.cpp

+	matplotlibcpp::clf();
+	matplotlibcpp::ylim(-0.05, 1.4);
+
+	std::map<std::string, std::string> erad_args;


warning: no header providing "std::map" is directly included [misc-include-cleaner]

src/problems/RadParticle/test_radparticle.cpp:16:

- #ifdef HAVE_PYTHON + #include <map> + #ifdef HAVE_PYTHON

github-actions · 2025-01-06T13:27:36Z

src/problems/RadParticle2D/test_radparticle_2D.cpp

+///
+
+#include "test_radparticle_2D.hpp"
+#include "QuokkaSimulation.hpp"


warning: included header test_radparticle_2D.hpp is not used directly [misc-include-cleaner]

Suggested change

#include "QuokkaSimulation.hpp"

#include "QuokkaSimulation.hpp"

github-actions · 2025-01-06T13:27:37Z

src/problems/RadParticle2D/test_radparticle_2D.cpp

+
+const double lum1 = 1.0;
+
+template <> struct quokka::EOS_Traits<ParticleProblem> {


warning: no header providing "quokka::EOS_Traits" is directly included [misc-include-cleaner]

src/problems/RadParticle2D/test_radparticle_2D.cpp:6:

+ #include "hydro/EOS.hpp"

github-actions · 2025-01-06T13:27:37Z

src/problems/RadParticle2D/test_radparticle_2D.cpp

+	static constexpr double gamma = 5. / 3.;
+};
+
+template <> struct Physics_Traits<ParticleProblem> {


warning: no header providing "Physics_Traits" is directly included [misc-include-cleaner]

src/problems/RadParticle2D/test_radparticle_2D.cpp:6:

+ #include "physics_info.hpp"

github-actions · 2025-01-06T13:27:37Z

src/problems/RadParticle2D/test_radparticle_2D.cpp

+	// face-centred
+	static constexpr bool is_mhd_enabled = false;
+	static constexpr int nGroups = nGroups_; // number of radiation groups
+	static constexpr UnitSystem unit_system = UnitSystem::CONSTANTS;


warning: no header providing "UnitSystem" is directly included [misc-include-cleaner]

static constexpr UnitSystem unit_system = UnitSystem::CONSTANTS; ^

…assInheritance

sonarqubecloud · 2025-01-13T01:36:53Z

Quality Gate passed

Issues
26 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
16.5% Duplication on New Code

See analysis details on SonarQube Cloud

src/simulation.hpp

+		// Redistribute particles after movement. This ensures particles are in the correct cells/processors for radiation deposition
+		// TODO(cch): I believe this is needed and missing this in the original code was a bug, but I don't understand why this was not caught earlier.
+		// Maybe the binary_orbit test was the only test for gravity and there was no multiple boxes in that test?
+		for (int lev = 0; lev <= finest_level; ++lev) {


### Description add `misc-include-cleaner` to exclusion list of .clang-tidy. This will get rid of warnings like `warning: no header providing "AMREX_GPU_HOST_DEVICE" is directly included` in clang-tidy-review. ### Related issues Should get rid of the `clang-tidy-review` failure in PR #827 . ### Checklist _Before this pull request can be reviewed, all of these tasks should be completed. Denote completed tasks with an `x` inside the square brackets `[ ]` in the Markdown source below:_ - [x] I have added a description (see above). - [x] I have added a link to any related issues (if applicable; see above). - [x] I have read the [Contributing Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md). - [ ] I have added tests for any new physics that this PR adds to the code. - [ ] *(For quokka-astro org members)* I have manually triggered the GPU tests with the magic comment `/azp run`.

chongchonghe and others added 30 commits November 26, 2024 21:33

copy RadParticle test from chong/RadParticle branch

f0a22f7

setup RadStreaming for particle test

5e39080

merge in RadParticles.hpp from RadPartcile branch

b7d5e0b

particle rad: step1

e88a5b1

update radparticles.hpp

e2a00e5

setup a fake DepositeParticleRadiation

b4a4bf5

tmp1

3084d6f

moved DepositeParticleRadiation to RadSystem

3d52fdc

cleanup

6d21fbe

revert to use SetRadEnergySource

5f85731

move SetRadEnergySource outside of operatorSplitSourceTerms

a42332d

so that SetRadEnergySource is called on all Fabs at a level

rename

908dcf3

move InitRadParticles to QuokkaSimulation

b107c48

minor

7d0c456

test: use CICParticle for radiation, working

fb104fe

update conversion in ParticleToMesh

dc2d1d7

update the calculation of src to exclude c

17c285f

tmp: define RadDeposition; not using it yet

4d42699

use RadParticles, instead of CICParticles, for radiating particles; p…

b700bf5

…assing tests

cleanup

eedc6c5

revert rad_sys.hpp: remove DepositeParticleRadiation

4c94349

cleanup

66c09fe

add current_time to RadDeposition

ce11740

remove do_rad_particles from RadSystem_Traits

ccabd66

define the RadParticle test for 1D problem

b0780b7

restore RadStreaming test

b79f43f

cleanup

31739a6

define RadParticle2D test

e7680ab

[pre-commit.ci] auto fixes from pre-commit.com hooks

547607d

for more information, see https://pre-commit.ci

add template problem_t to RadParticleContainer

c5db9b9

github-actions bot reviewed Dec 23, 2024

View reviewed changes

chongchonghe and others added 3 commits December 23, 2024 19:06

define getParticleContainer()

9757924

update particle_3D test

0e5562d

[pre-commit.ci] auto fixes from pre-commit.com hooks

d820ffc

for more information, see https://pre-commit.ci

github-actions bot reviewed Dec 23, 2024

View reviewed changes

add include

772bd3d

github-actions bot reviewed Dec 30, 2024

View reviewed changes

add more includes

86c8e6e

github-actions bot reviewed Dec 30, 2024

View reviewed changes

chongchonghe and others added 3 commits December 30, 2024 12:08

more includes

2b3ab8f

cleanup and fix bugs

4685c9c

[pre-commit.ci] auto fixes from pre-commit.com hooks

f3deda6

for more information, see https://pre-commit.ci

github-actions bot reviewed Dec 30, 2024

View reviewed changes

set RadParticle to run in 1D only

390e2d2

github-actions bot reviewed Dec 31, 2024

View reviewed changes

chongchonghe added 2 commits January 2, 2025 23:57

fix minor bug

009cc67

address git-action comments

586842c

github-actions bot reviewed Jan 6, 2025

View reviewed changes

add misc-include-cleaner to exclusion

3fa92d5

chongchonghe mentioned this pull request Jan 13, 2025

exclude misc-include-cleaner in clang-tidy #848

Merged

5 tasks

chongchonghe added 2 commits January 13, 2025 12:32

Merge branch 'development' into chong/PhyParticlesClassInheritance

fced4a6

Merge branch 'chong/remove-include-cleaner' into chong/PhyParticlesCl…

be77d62

…assInheritance

github-advanced-security bot found potential problems Jan 13, 2025

View reviewed changes


		const double lum1 = 1.0;

		template <> struct quokka::EOS_Traits<ParticleProblem> {

	#include "QuokkaSimulation.hpp"
	#include "QuokkaSimulation.hpp"

	#include "radiation/radiation_system.hpp"
	#include "radiation/radiation_system.hpp"

	constexpr int nvars = RadSystem<ParticleProblem>::nvar_;
	constexpr int nvars = 0 = RadSystem<ParticleProblem>::nvar_;

	const double total_Erad_over_vol = sim.state_new_cc_[0].sum(RadSystem<ParticleProblem>::radEnergy_index);
	const double total_Erad_over_vol = NAN = sim.state_new_cc_[0].sum(RadSystem<ParticleProblem>::radEnergy_index);

New particle interface using derived classes #827

Are you sure you want to change the base?

New particle interface using derived classes #827

Conversation

chongchonghe commented Dec 19, 2024 • edited Loading

Description

Core Components

1. PhysicsParticleDescriptor (Base Class)

2. Concrete Descriptor Classes

3. PhysicsParticleRegister

Usage

1. Creating and Registering Particles

2. Using the Interface

Key Features

Adding a New Particle Type

New test problems

Related issues

Checklist

github-actions bot left a comment

Choose a reason for hiding this comment

github-actions bot left a comment

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot Dec 23, 2024

Choose a reason for hiding this comment

github-actions bot left a comment

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot left a comment

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot left a comment

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

github-actions bot Dec 30, 2024

Choose a reason for hiding this comment

chongchonghe commented Dec 19, 2024 •

edited

Loading

chongchonghe commented Dec 31, 2024 •

edited

Loading