Rename RadhydroSimulation class to QuokkaSimulation (#702)

### Description

What's changed in the PR:
- Renamed `RadhydroSimulation` class to `QuokkaSimulation` in all
occurances inside src/.
- Renamed `RadhydroSimulation.cpp/.hpp` to `QuokkaSimulation.cpp/.hpp` 

Why? This is the main simulation class that does all of the physics,
including HD, gravity, radiation, MHD, etc. It should be given a more
general and inclusive name to avoid the confusion caused by the name
`RadhydroSimulation`. See #428

### Related issues

Addressed issue #428 

### 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 see (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.
- [x] I have tested this PR on my local computer and all tests pass.
- [x] I have manually triggered the GPU tests with the magic comment
`/azp run`.
- [x] I have requested a reviewer for this PR.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.cpp

@@ -0,0 +1 @@
+#include "QuokkaSimulation.hpp"

src/linear_advection/AdvectionSimulation.hpp

@@ -63,8 +63,8 @@ template <typename problem_t> class AdvectionSimulation : public AMRSimulation<p
 	void computeMaxSignalLocal(int level) override;
 	auto computeExtraPhysicsTimestep(int level) -> amrex::Real override;
 	void preCalculateInitialConditions() override;
-	void setInitialConditionsOnGrid(quokka::grid grid_elem) override;
-	void setInitialConditionsOnGridFaceVars(quokka::grid grid_elem) override;
+	void setInitialConditionsOnGrid(quokka::grid const &grid_elem) override;
+	void setInitialConditionsOnGridFaceVars(quokka::grid const &grid_elem) override;
 	void createInitialParticles() override;
 	void advanceSingleTimestepAtLevel(int lev, amrex::Real time, amrex::Real dt_lev, int /*ncycle*/) override;
 	void computeBeforeTimestep() override;
@@ -137,13 +137,13 @@ template <typename problem_t> void AdvectionSimulation<problem_t>::preCalculateI
 	// user should implement using problem-specific template specialization
 }
 
-template <typename problem_t> void AdvectionSimulation<problem_t>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <typename problem_t> void AdvectionSimulation<problem_t>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// default empty implementation
 	// user should implement using problem-specific template specialization
 }
 
-template <typename problem_t> void AdvectionSimulation<problem_t>::setInitialConditionsOnGridFaceVars(quokka::grid grid_elem)
+template <typename problem_t> void AdvectionSimulation<problem_t>::setInitialConditionsOnGridFaceVars(quokka::grid const &grid_elem)
 {
 	// default empty implementation
 	// user should implement using problem-specific template specialization

src/problems/Advection/test_advection.cpp

@@ -47,7 +47,7 @@ AMREX_GPU_DEVICE void ComputeExactSolution(int i, int j, int k, int n, amrex::Ar
 	exact_arr(i, j, k, n) = value;
 }
 
-template <> void AdvectionSimulation<SawtoothProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void AdvectionSimulation<SawtoothProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;

src/problems/Advection2D/test_advection2d.cpp

@@ -57,7 +57,7 @@ AMREX_GPU_DEVICE AMREX_FORCE_INLINE auto exactSolutionAtIndex(int i, int j, amre
 	return rho;
 }
 
-template <> void AdvectionSimulation<SquareProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void AdvectionSimulation<SquareProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;

src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp

@@ -46,7 +46,7 @@ AMREX_GPU_DEVICE void ComputeExactSolution(int i, int j, int k, int n, amrex::Ar
 	exact_arr(i, j, k, n) = dens;
 }
 
-template <> void AdvectionSimulation<SemiellipseProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void AdvectionSimulation<SemiellipseProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;

src/problems/BinaryOrbitCIC/binary_orbit.cpp

@@ -23,7 +23,7 @@
 
 #include "AMReX_REAL.H"
 #include "AMReX_ccse-mpi.H"
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "binary_orbit.hpp"
 #include "hydro/hydro_system.hpp"
 #include <algorithm>
@@ -56,7 +56,7 @@ template <> struct SimulationData<BinaryOrbit> {
 	std::vector<amrex::ParticleReal> dist{};
 };
 
-template <> void RadhydroSimulation<BinaryOrbit>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<BinaryOrbit>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	const amrex::Box &indexRange = grid_elem.indexRange_;
 	const amrex::Array4<double> &state_cc = grid_elem.array_;
@@ -72,15 +72,15 @@ template <> void RadhydroSimulation<BinaryOrbit>::setInitialConditionsOnGrid(quo
 	});
 }
 
-template <> void RadhydroSimulation<BinaryOrbit>::createInitialParticles()
+template <> void QuokkaSimulation<BinaryOrbit>::createInitialParticles()
 {
 	// read particles from ASCII file
 	const int nreal_extra = 4; // mass vx vy vz
 	CICParticles->SetVerbose(1);
 	CICParticles->InitFromAsciiFile("BinaryOrbit_particles.txt", nreal_extra, nullptr);
 }
 
-template <> void RadhydroSimulation<BinaryOrbit>::ComputeDerivedVar(int lev, std::string const &dname, amrex::MultiFab &mf, const int ncomp_cc_in) const
+template <> void QuokkaSimulation<BinaryOrbit>::ComputeDerivedVar(int lev, std::string const &dname, amrex::MultiFab &mf, const int ncomp_cc_in) const
 {
 	// compute derived variables and save in 'mf'
 	if (dname == "gpot") {
@@ -91,7 +91,7 @@ template <> void RadhydroSimulation<BinaryOrbit>::ComputeDerivedVar(int lev, std
 	}
 }
 
-template <> void RadhydroSimulation<BinaryOrbit>::computeAfterTimestep()
+template <> void QuokkaSimulation<BinaryOrbit>::computeAfterTimestep()
 {
 	// every N cycles, save particle statistics
 	static int cycle = 1;
@@ -167,7 +167,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<BinaryOrbit> sim(BCs_cc);
+	QuokkaSimulation<BinaryOrbit> sim(BCs_cc);
 	sim.doPoissonSolve_ = 1; // enable self-gravity
 	sim.initDt_ = 1.0e3;	 // s
 

src/problems/Cooling/test_cooling.cpp

@@ -13,7 +13,7 @@
 #include "AMReX_GpuDevice.H"
 #include "AMReX_TableData.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "radiation/radiation_system.hpp"
 
 using amrex::Real;
@@ -53,7 +53,7 @@ const int kmin = 0;
 const int kmax = 16;
 Real const A = 0.05 / kmax;
 
-template <> void RadhydroSimulation<CoolingTest>::preCalculateInitialConditions()
+template <> void QuokkaSimulation<CoolingTest>::preCalculateInitialConditions()
 {
 	// generate random phases
 	amrex::Array<int, 3> tlo{kmin, kmin, kmin}; // lower bounds
@@ -81,7 +81,7 @@ template <> void RadhydroSimulation<CoolingTest>::preCalculateInitialConditions(
 	amrex::Gpu::streamSynchronize();
 }
 
-template <> void RadhydroSimulation<CoolingTest>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<CoolingTest>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// set initial conditions
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -195,7 +195,7 @@ auto problem_main() -> int
 #endif
 	}
 
-	RadhydroSimulation<CoolingTest> sim(BCs_cc);
+	QuokkaSimulation<CoolingTest> sim(BCs_cc);
 
 	// Standard PPM gives unphysically enormous temperatures when used for
 	// this problem (e.g., ~1e14 K or higher), but can be fixed by

src/problems/FCQuantities/test_fc_quantities.cpp

@@ -16,7 +16,7 @@
 #include "AMReX_Print.H"
 #include "AMReX_REAL.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "grid.hpp"
 #include "physics_info.hpp"
 #include "test_fc_quantities.hpp"
@@ -71,7 +71,7 @@ AMREX_GPU_DEVICE void computeWaveSolution(int i, int j, int k, amrex::Array4<amr
 	state(i, j, k, HydroSystem<FCQuantities>::internalEnergy_index) = Eint;
 }
 
-template <> void RadhydroSimulation<FCQuantities>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<FCQuantities>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract grid information
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -89,7 +89,7 @@ template <> void RadhydroSimulation<FCQuantities>::setInitialConditionsOnGrid(qu
 	});
 }
 
-template <> void RadhydroSimulation<FCQuantities>::setInitialConditionsOnGridFaceVars(quokka::grid grid_elem)
+template <> void QuokkaSimulation<FCQuantities>::setInitialConditionsOnGridFaceVars(quokka::grid const &grid_elem)
 {
 	// extract grid information
 	const amrex::Array4<double> &state = grid_elem.array_;
@@ -155,12 +155,12 @@ auto problem_main() -> int
 		}
 	}
 
-	RadhydroSimulation<FCQuantities> sim_write(BCs_cc, BCs_fc);
+	QuokkaSimulation<FCQuantities> sim_write(BCs_cc, BCs_fc);
 	sim_write.setInitialConditions();
 	amrex::Vector<amrex::Array<amrex::MultiFab, AMREX_SPACEDIM>> const &state_new_fc_write = sim_write.getNewMF_fc();
 	amrex::Print() << "\n";
 
-	RadhydroSimulation<FCQuantities> sim_restart(BCs_cc, BCs_fc);
+	QuokkaSimulation<FCQuantities> sim_restart(BCs_cc, BCs_fc);
 	sim_restart.setChkFile("chk00000");
 	sim_restart.setInitialConditions();
 	amrex::Vector<amrex::Array<amrex::MultiFab, AMREX_SPACEDIM>> const &state_new_fc_restart = sim_restart.getNewMF_fc();

src/problems/HydroBlast2D/test_hydro2d_blast.cpp

@@ -18,7 +18,7 @@
 #include "AMReX_REAL.H"
 #include "AMReX_TagBox.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "hydro/hydro_system.hpp"
 #include "test_hydro2d_blast.hpp"
 
@@ -42,7 +42,7 @@ template <> struct Physics_Traits<BlastProblem> {
 	static constexpr int nGroups = 1; // number of radiation groups
 };
 
-template <> void RadhydroSimulation<BlastProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<BlastProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -94,7 +94,7 @@ template <> void RadhydroSimulation<BlastProblem>::setInitialConditionsOnGrid(qu
 	});
 }
 
-template <> void RadhydroSimulation<BlastProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
+template <> void QuokkaSimulation<BlastProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
 {
 	// tag cells for refinement
 
@@ -143,7 +143,7 @@ auto problem_main() -> int
 		return false;
 	};
 
-	const int ncomp_cc = RadhydroSimulation<BlastProblem>::nvarTotal_cc_;
+	const int ncomp_cc = QuokkaSimulation<BlastProblem>::nvarTotal_cc_;
 	amrex::Vector<amrex::BCRec> BCs_cc(ncomp_cc);
 	for (int n = 0; n < ncomp_cc; ++n) {
 		for (int i = 0; i < AMREX_SPACEDIM; ++i) {
@@ -164,7 +164,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<BlastProblem> sim(BCs_cc);
+	QuokkaSimulation<BlastProblem> sim(BCs_cc);
 
 	sim.stopTime_ = 0.1; // 1.5;
 	sim.cflNumber_ = 0.3;

src/problems/HydroBlast3D/test_hydro3d_blast.cpp

@@ -15,7 +15,7 @@
 #include "AMReX_Print.H"
 #include "AMReX_SPACE.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "hydro/hydro_system.hpp"
 #include "radiation/radiation_system.hpp"
 
@@ -52,14 +52,14 @@ template <> struct Physics_Traits<SedovProblem> {
 const double rho = 1.0;	   // g cm^-3
 double E_blast = 0.851072; // ergs
 
-template <> void RadhydroSimulation<SedovProblem>::preCalculateInitialConditions()
+template <> void QuokkaSimulation<SedovProblem>::preCalculateInitialConditions()
 {
 	if constexpr (!simulate_full_box) {
 		E_blast /= 8.0; // only one octant, so 1/8 of the total energy
 	}
 }
 
-template <> void RadhydroSimulation<SedovProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<SedovProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// initialize a Sedov test problem using parameters from
 	// Richard Klein and J. Bolstad
@@ -115,7 +115,7 @@ template <> void RadhydroSimulation<SedovProblem>::setInitialConditionsOnGrid(qu
 	});
 }
 
-template <> void RadhydroSimulation<SedovProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
+template <> void QuokkaSimulation<SedovProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
 {
 	// tag cells for refinement
 
@@ -150,7 +150,7 @@ template <> void RadhydroSimulation<SedovProblem>::ErrorEst(int lev, amrex::TagB
 	}
 }
 
-template <> void RadhydroSimulation<SedovProblem>::computeAfterEvolve(amrex::Vector<amrex::Real> &initSumCons)
+template <> void QuokkaSimulation<SedovProblem>::computeAfterEvolve(amrex::Vector<amrex::Real> &initSumCons)
 {
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &dx0 = geom[0].CellSizeArray();
 	amrex::Real const vol = AMREX_D_TERM(dx0[0], *dx0[1], *dx0[2]);
@@ -254,7 +254,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<SedovProblem> sim(BCs_cc);
+	QuokkaSimulation<SedovProblem> sim(BCs_cc);
 
 	sim.reconstructionOrder_ = 3; // 2=PLM, 3=PPM
 	sim.stopTime_ = 1.0;	      // seconds

src/problems/HydroContact/test_hydro_contact.cpp

@@ -12,7 +12,7 @@
 #include "AMReX_MultiFab.H"
 #include "AMReX_ParmParse.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "hydro/hydro_system.hpp"
 #include "radiation/radiation_system.hpp"
 #include "test_hydro_contact.hpp"
@@ -40,7 +40,7 @@ template <> struct Physics_Traits<ContactProblem> {
 
 constexpr double v_contact = 0.0; // contact wave velocity
 
-template <> void RadhydroSimulation<ContactProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<ContactProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -83,8 +83,8 @@ template <> void RadhydroSimulation<ContactProblem>::setInitialConditionsOnGrid(
 }
 
 template <>
-void RadhydroSimulation<ContactProblem>::computeReferenceSolution(amrex::MultiFab &ref, amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &dx,
-								  amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &prob_lo)
+void QuokkaSimulation<ContactProblem>::computeReferenceSolution(amrex::MultiFab &ref, amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &dx,
+								amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &prob_lo)
 {
 	for (amrex::MFIter iter(ref); iter.isValid(); ++iter) {
 		const amrex::Box &indexRange = iter.validbox();
@@ -195,7 +195,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<ContactProblem> sim(BCs_cc);
+	QuokkaSimulation<ContactProblem> sim(BCs_cc);
 
 	sim.stopTime_ = 2.0;
 	sim.cflNumber_ = 0.8;

src/problems/HydroHighMach/test_hydro_highmach.cpp

@@ -12,7 +12,7 @@
 #include "AMReX_MultiFab.H"
 #include "AMReX_ParmParse.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "hydro/hydro_system.hpp"
 #include "util/fextract.hpp"
 #ifdef HAVE_PYTHON
@@ -45,7 +45,7 @@ template <> struct Physics_Traits<HighMachProblem> {
 	static constexpr int nGroups = 1; // number of radiation groups
 };
 
-template <> void RadhydroSimulation<HighMachProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<HighMachProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -81,8 +81,8 @@ template <> void RadhydroSimulation<HighMachProblem>::setInitialConditionsOnGrid
 }
 
 template <>
-void RadhydroSimulation<HighMachProblem>::computeReferenceSolution(amrex::MultiFab &ref, amrex::GpuArray<Real, AMREX_SPACEDIM> const &dx,
-								   amrex::GpuArray<Real, AMREX_SPACEDIM> const &prob_lo)
+void QuokkaSimulation<HighMachProblem>::computeReferenceSolution(amrex::MultiFab &ref, amrex::GpuArray<Real, AMREX_SPACEDIM> const &dx,
+								 amrex::GpuArray<Real, AMREX_SPACEDIM> const &prob_lo)
 {
 
 	// extract solution
@@ -258,7 +258,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<HighMachProblem> sim(BCs_cc);
+	QuokkaSimulation<HighMachProblem> sim(BCs_cc);
 
 	sim.computeReferenceSolution_ = true;
 

src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp

@@ -15,7 +15,7 @@
 #include "AMReX_ParmParse.H"
 #include "AMReX_Print.H"
 
-#include "RadhydroSimulation.hpp"
+#include "QuokkaSimulation.hpp"
 #include "hydro/hydro_system.hpp"
 #include "test_hydro2d_kh.hpp"
 
@@ -43,7 +43,7 @@ template <> struct Physics_Traits<KelvinHelmholzProblem> {
 	static constexpr int nGroups = 1; // number of radiation groups
 };
 
-template <> void RadhydroSimulation<KelvinHelmholzProblem>::setInitialConditionsOnGrid(quokka::grid grid_elem)
+template <> void QuokkaSimulation<KelvinHelmholzProblem>::setInitialConditionsOnGrid(quokka::grid const &grid_elem)
 {
 	// extract variables required from the geom object
 	amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> dx = grid_elem.dx_;
@@ -87,7 +87,7 @@ template <> void RadhydroSimulation<KelvinHelmholzProblem>::setInitialConditions
 	});
 }
 
-template <> void RadhydroSimulation<KelvinHelmholzProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
+template <> void QuokkaSimulation<KelvinHelmholzProblem>::ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real /*time*/, int /*ngrow*/)
 {
 	// tag cells for refinement
 
@@ -132,7 +132,7 @@ auto problem_main() -> int
 	}
 
 	// Problem initialization
-	RadhydroSimulation<KelvinHelmholzProblem> sim(BCs_cc);
+	QuokkaSimulation<KelvinHelmholzProblem> sim(BCs_cc);
 
 	sim.stopTime_ = 1.5;
 	sim.cflNumber_ = 0.4;