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Save additional node variables in SaveSolutionCallback (#2298)
* Save additional node variables in `SaveSolutionCallback` * dispatch functions correctly, document new dict * use vorticity computation * continue * working version * parallel (to be tested!) * clean up * mpi tests * 3d fix * 3d * access non-exported func * comment * remove doubled method * simplify * use singular * need to figure out which elixirs are MPI-parallel, but single I/O * add example for coverage * Update examples/tree_2d_dgsem/elixir_advection_timeintegration_adaptive.jl * not needed, mpi tests windows tiem out * send data * fmt * add ":limiting_coefficient" as "extra_node_variables" * Subcell + CNS * fmt * fix path * test vals * Update src/callbacks_step/save_solution.jl * comments * Update src/solvers/dg.jl Co-authored-by: Benjamin Bolm <[email protected]> * docu + news entry * fix merge errors * fmt * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> --------- Co-authored-by: Benjamin Bolm <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]>
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‎NEWS.md

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@@ -9,8 +9,18 @@ for human readability.
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#### Added
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- Arbitrary solution-dependent quantities can now be saved in the `SaveSolutionCallback` (and thus later on visualized) ([#2298]).
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#### Changed
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- When using the `VolumeIntegralSubcellLimiting` with the `SubcellLimiterIDP` the
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`:limiting_coefficient` must be explicitly provided to the `SaveSolutionCallback` via
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```julia
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save_sol_cb = SaveSolutionCallback(interval = 42,
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extra_node_variables = (:limiting_coefficient,))
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```
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i.e., is no longer automatically saved ([#2298]).
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#### Deprecated
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#### Removed

‎examples/p4est_2d_dgsem/elixir_euler_sedov_blast_wave_sc_subcell.jl

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@@ -80,7 +80,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 300,
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save_initial_solution = true,
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save_final_solution = true)
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save_final_solution = true,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.5)
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‎examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder_sc_subcell.jl

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@@ -144,7 +144,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 1000,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.8)
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‎examples/p4est_2d_dgsem/elixir_navierstokes_vortex_street.jl

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@@ -102,10 +102,52 @@ analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
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alive_callback = AliveCallback(analysis_interval = analysis_interval)
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# Add `:vorticity` to `extra_node_variables` tuple ...
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extra_node_variables = (:vorticity,)
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# ... and specify the function `get_node_variable` for this symbol,
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# with first argument matching the symbol (turned into a type via `Val`) for dispatching.
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# Note that for parabolic(-extended) equations, `equations_parabolic` and `cache_parabolic`
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# must be declared as the last two arguments of the function to match the expected signature.
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function Trixi.get_node_variable(::Val{:vorticity}, u, mesh, equations, dg, cache,
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equations_parabolic, cache_parabolic)
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n_nodes = nnodes(dg)
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n_elements = nelements(dg, cache)
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# By definition, the variable must be provided at every node of every element!
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# Otherwise, the `SaveSolutionCallback` will crash.
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vorticity_array = zeros(eltype(cache.elements),
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n_nodes, n_nodes, # equivalent: `ntuple(_ -> n_nodes, ndims(mesh))...,`
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n_elements)
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@unpack viscous_container = cache_parabolic
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@unpack gradients = viscous_container
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gradients_x, gradients_y = gradients
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# We can accelerate the computation by thread-parallelizing the loop over elements
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# by using the `@threaded` macro.
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Trixi.@threaded for element in eachelement(dg, cache)
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for j in eachnode(dg), i in eachnode(dg)
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u_node = get_node_vars(u, equations, dg, i, j, element)
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gradients_1 = get_node_vars(gradients_x, equations_parabolic, dg,
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i, j, element)
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gradients_2 = get_node_vars(gradients_y, equations_parabolic, dg,
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i, j, element)
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vorticity_nodal = vorticity(u_node, (gradients_1, gradients_2),
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equations_parabolic)
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vorticity_array[i, j, element] = vorticity_nodal
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end
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end
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return vorticity_array
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end
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save_solution = SaveSolutionCallback(dt = 1.0,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = extra_node_variables) # Supply the additional `extra_node_variables` here
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callbacks = CallbackSet(summary_callback,
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analysis_callback,

‎examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl

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@@ -132,9 +132,8 @@ function Trixi.analyze(::Val{:energy_potential}, du, u_euler, t,
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u_gravity) do u, i, j, element,
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equations_euler, dg,
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equations_gravity, u_gravity
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u_euler_local = Trixi.get_node_vars(u_euler, equations_euler, dg, i, j, element)
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u_gravity_local = Trixi.get_node_vars(u_gravity, equations_gravity, dg, i, j,
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element)
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u_euler_local = get_node_vars(u_euler, equations_euler, dg, i, j, element)
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u_gravity_local = get_node_vars(u_gravity, equations_gravity, dg, i, j, element)
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# OBS! subtraction is specific to Jeans instability test where rho0 = 1.5e7
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# For formula of potential energy see
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# "Galactic Dynamics" by Binney and Tremaine, 2nd ed., equation (2.18)

‎examples/structured_2d_dgsem/elixir_euler_sedov_blast_wave_sc_subcell.jl

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@@ -95,7 +95,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.6)
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‎examples/t8code_3d_dgsem/elixir_euler_ec.jl

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@@ -68,9 +68,37 @@ analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
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alive_callback = AliveCallback(analysis_interval = analysis_interval)
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# Add `:thermodynamic_entropy` to `extra_node_variables` tuple ...
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extra_node_variables = (:thermodynamic_entropy,)
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# ... and specify the function `get_node_variable` for this symbol,
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# with first argument matching the symbol (turned into a type via `Val`) for dispatching.
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function Trixi.get_node_variable(::Val{:thermodynamic_entropy}, u, mesh, equations,
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dg, cache)
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n_nodes = nnodes(dg)
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n_elements = nelements(dg, cache)
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# By definition, the variable must be provided at every node of every element!
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# Otherwise, the `SaveSolutionCallback` will crash.
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entropy_array = zeros(eltype(cache.elements),
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ntuple(_ -> n_nodes, ndims(mesh))..., # equivalent: `n_nodes, n_nodes, n_nodes`
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n_elements)
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# We can accelerate the computation by thread-parallelizing the loop over elements
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# by using the `@threaded` macro.
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Trixi.@threaded for element in eachelement(dg, cache)
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for k in eachnode(dg), j in eachnode(dg), i in eachnode(dg)
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u_node = get_node_vars(u, equations, dg, i, j, k, element)
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entropy_array[i, j, k, element] = Trixi.entropy_thermodynamic(u_node, equations)
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end
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end
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return entropy_array
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end
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true)
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save_final_solution = true,
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extra_node_variables = extra_node_variables) # Supply the additional `extra_node_variables` here
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stepsize_callback = StepsizeCallback(cfl = 1.0)
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‎examples/tree_2d_dgsem/elixir_euler_blast_wave_amr.jl

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@@ -69,10 +69,40 @@ analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
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alive_callback = AliveCallback(analysis_interval = analysis_interval)
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# Add `:mach` to `extra_node_variables` tuple ...
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extra_node_variables = (:mach,)
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# ... and specify the function `get_node_variable` for this symbol,
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# with first argument matching the symbol (turned into a type via `Val`) for dispatching.
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function Trixi.get_node_variable(::Val{:mach}, u, mesh, equations, dg, cache)
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n_nodes = nnodes(dg)
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n_elements = nelements(dg, cache)
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# By definition, the variable must be provided at every node of every element!
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# Otherwise, the `SaveSolutionCallback` will crash.
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mach_array = zeros(eltype(cache.elements),
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n_nodes, n_nodes, # equivalent: `ntuple(_ -> n_nodes, ndims(mesh))...,`
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n_elements)
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# We can accelerate the computation by thread-parallelizing the loop over elements
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# by using the `@threaded` macro.
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Trixi.@threaded for element in eachelement(dg, cache)
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for j in eachnode(dg), i in eachnode(dg)
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u_node = get_node_vars(u, equations, dg, i, j, element)
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rho, v1, v2, p = prim2cons(u_node, equations)
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c = sqrt(equations.gamma * p / rho) # speed of sound
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v_magnitude = sqrt(v1^2 + v2^2)
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mach_array[i, j, element] = v_magnitude / c
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end
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end
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return mach_array
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end
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = extra_node_variables) # Supply the additional `extra_node_variables` here
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amr_indicator = IndicatorHennemannGassner(semi,
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alpha_max = 0.5,

‎examples/tree_2d_dgsem/elixir_euler_blast_wave_sc_subcell_nonperiodic.jl

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@@ -77,7 +77,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.3)
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‎examples/tree_2d_dgsem/elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl

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@@ -66,7 +66,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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save_restart = SaveRestartCallback(interval = 1000,
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save_final_restart = true)

‎examples/tree_2d_dgsem/elixir_euler_sedov_blast_wave_sc_subcell.jl

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@@ -77,7 +77,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 1000,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.4)
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‎examples/tree_2d_dgsem/elixir_euler_shockcapturing_subcell.jl

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@@ -69,7 +69,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(dt = 0.1,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.6)
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‎examples/tree_2d_dgsem/elixir_euler_vortex_amr.jl

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@@ -143,10 +143,39 @@ analysis_callback = AnalysisCallback(semi, interval = analysis_interval,
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alive_callback = AliveCallback(analysis_interval = analysis_interval)
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# Add `:temperature` to `extra_node_variables` tuple ...
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extra_node_variables = (:temperature,)
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# ... and specify the function `get_node_variable` for this symbol,
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# with first argument matching the symbol (turned into a type via `Val`) for dispatching.
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function Trixi.get_node_variable(::Val{:temperature}, u, mesh, equations, dg, cache)
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n_nodes = nnodes(dg)
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n_elements = nelements(dg, cache)
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# By definition, the variable must be provided at every node of every element!
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# Otherwise, the `SaveSolutionCallback` will crash.
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temp_array = zeros(eltype(cache.elements),
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n_nodes, n_nodes, # equivalent: `ntuple(_ -> n_nodes, ndims(mesh))...,`
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n_elements)
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# We can accelerate the computation by thread-parallelizing the loop over elements
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# by using the `@threaded` macro.
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Trixi.@threaded for element in eachelement(dg, cache)
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for j in eachnode(dg), i in eachnode(dg)
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u_node = get_node_vars(u, equations, dg, i, j, element)
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rho, _, _, p = prim2cons(u_node, equations)
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temp = p / rho # ideal gas equation with R = 1
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temp_array[i, j, element] = temp
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end
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end
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return temp_array
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end
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save_solution = SaveSolutionCallback(interval = 50,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = extra_node_variables) # Supply the additional `extra_node_variables` here
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amr_controller = ControllerThreeLevel(semi, TrixiExtension.IndicatorVortex(semi),
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base_level = 3,

‎examples/tree_2d_dgsem/elixir_eulermulti_shock_bubble_shockcapturing_subcell_minmax.jl

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@@ -119,7 +119,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 600,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.4)
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‎examples/tree_2d_dgsem/elixir_eulermulti_shock_bubble_shockcapturing_subcell_positivity.jl

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@@ -120,7 +120,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 300,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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stepsize_callback = StepsizeCallback(cfl = 0.9)
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‎examples/tree_2d_dgsem/elixir_mhd_shockcapturing_subcell.jl

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@@ -82,7 +82,8 @@ alive_callback = AliveCallback(analysis_interval = analysis_interval)
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save_solution = SaveSolutionCallback(interval = 100,
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save_initial_solution = true,
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save_final_solution = true,
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solution_variables = cons2prim)
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solution_variables = cons2prim,
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extra_node_variables = (:limiting_coefficient,))
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cfl = 0.4
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stepsize_callback = StepsizeCallback(cfl = cfl)

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