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SimonCan authored Jan 4, 2024

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2 parents dbf2aea + ad384c6 commit 307f68a
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2 changes: 1 addition & 1 deletion .github/workflows/SpellCheck.yml
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@@ -10,4 +10,4 @@ jobs:
- name: Checkout Actions Repository
uses: actions/checkout@v4
- name: Check spelling
uses: crate-ci/[email protected].23
uses: crate-ci/[email protected].26
6 changes: 6 additions & 0 deletions NEWS.md
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@@ -4,6 +4,12 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
used in the Julia ecosystem. Notable changes will be documented in this file
for human readability.

## Changes in the v0.6 lifecycle

#### Added
- AMR for hyperbolic-parabolic equations on 3D `P4estMesh`
- `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D`

## Changes when updating to v0.6 from v0.5.x

#### Added
4 changes: 3 additions & 1 deletion Project.toml
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@@ -1,12 +1,13 @@
name = "Trixi"
uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
version = "0.6.5-pre"
version = "0.6.6-pre"

[deps]
CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
@@ -54,6 +55,7 @@ TrixiMakieExt = "Makie"
CodeTracking = "1.0.5"
ConstructionBase = "1.3"
DataStructures = "0.18.15"
DiffEqBase = "6 - 6.143"
DiffEqCallbacks = "2.25"
EllipsisNotation = "1.0"
FillArrays = "0.13.2, 1"
113 changes: 113 additions & 0 deletions examples/p4est_3d_dgsem/elixir_navierstokes_blast_wave_amr.jl
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@@ -0,0 +1,113 @@

using OrdinaryDiffEq
using Trixi

###############################################################################
# semidiscretization of the compressible Navier-Stokes equations

# TODO: parabolic; unify names of these accessor functions
prandtl_number() = 0.72
mu() = 6.25e-4 # equivalent to Re = 1600

equations = CompressibleEulerEquations3D(1.4)
equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
Prandtl = prandtl_number())

function initial_condition_3d_blast_wave(x, t, equations::CompressibleEulerEquations3D)
rho_c = 1.0
p_c = 1.0
u_c = 0.0

rho_o = 0.125
p_o = 0.1
u_o = 0.0

rc = 0.5
r = sqrt(x[1]^2 + x[2]^2 + x[3]^2)
if r < rc
rho = rho_c
v1 = u_c
v2 = u_c
v3 = u_c
p = p_c
else
rho = rho_o
v1 = u_o
v2 = u_o
v3 = u_o
p = p_o
end

return prim2cons(SVector(rho, v1, v2, v3, p), equations)
end
initial_condition = initial_condition_3d_blast_wave

surface_flux = flux_lax_friedrichs
volume_flux = flux_ranocha
polydeg = 3
basis = LobattoLegendreBasis(polydeg)
indicator_sc = IndicatorHennemannGassner(equations, basis,
alpha_max = 1.0,
alpha_min = 0.001,
alpha_smooth = true,
variable = density_pressure)
volume_integral = VolumeIntegralShockCapturingHG(indicator_sc;
volume_flux_dg = volume_flux,
volume_flux_fv = surface_flux)

solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
volume_integral = volume_integral)

coordinates_min = (-1.0, -1.0, -1.0) .* pi
coordinates_max = (1.0, 1.0, 1.0) .* pi

trees_per_dimension = (4, 4, 4)

mesh = P4estMesh(trees_per_dimension, polydeg = 3,
coordinates_min = coordinates_min, coordinates_max = coordinates_max,
periodicity = (true, true, true), initial_refinement_level = 1)

semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic),
initial_condition, solver)

###############################################################################
# ODE solvers, callbacks etc.

tspan = (0.0, 0.8)
ode = semidiscretize(semi, tspan)

summary_callback = SummaryCallback()

analysis_interval = 100
analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
save_solution = SaveSolutionCallback(interval = analysis_interval,
save_initial_solution = true,
save_final_solution = true,
solution_variables = cons2prim)

amr_indicator = IndicatorLöhner(semi, variable = Trixi.density)

amr_controller = ControllerThreeLevel(semi, amr_indicator,
base_level = 0,
med_level = 1, med_threshold = 0.05,
max_level = 3, max_threshold = 0.1)
amr_callback = AMRCallback(semi, amr_controller,
interval = 10,
adapt_initial_condition = true,
adapt_initial_condition_only_refine = true)

alive_callback = AliveCallback(analysis_interval = analysis_interval)

callbacks = CallbackSet(summary_callback,
analysis_callback,
alive_callback,
amr_callback,
save_solution)

###############################################################################
# run the simulation

time_int_tol = 1e-8
sol = solve(ode, RDPK3SpFSAL49(); abstol = time_int_tol, reltol = time_int_tol,
ode_default_options()..., callback = callbacks)
summary_callback() # print the timer summary
106 changes: 106 additions & 0 deletions examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl
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@@ -0,0 +1,106 @@

using OrdinaryDiffEq
using Trixi

###############################################################################
# semidiscretization of the compressible Navier-Stokes equations

# TODO: parabolic; unify names of these accessor functions
prandtl_number() = 0.72
mu() = 6.25e-4 # equivalent to Re = 1600

equations = CompressibleEulerEquations3D(1.4)
equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
Prandtl = prandtl_number())

"""
initial_condition_taylor_green_vortex(x, t, equations::CompressibleEulerEquations3D)
The classical Taylor-Green vortex.
"""
function initial_condition_taylor_green_vortex(x, t,
equations::CompressibleEulerEquations3D)
A = 1.0 # magnitude of speed
Ms = 0.1 # maximum Mach number

rho = 1.0
v1 = A * sin(x[1]) * cos(x[2]) * cos(x[3])
v2 = -A * cos(x[1]) * sin(x[2]) * cos(x[3])
v3 = 0.0
p = (A / Ms)^2 * rho / equations.gamma # scaling to get Ms
p = p +
1.0 / 16.0 * A^2 * rho *
(cos(2 * x[1]) * cos(2 * x[3]) + 2 * cos(2 * x[2]) + 2 * cos(2 * x[1]) +
cos(2 * x[2]) * cos(2 * x[3]))

return prim2cons(SVector(rho, v1, v2, v3, p), equations)
end
initial_condition = initial_condition_taylor_green_vortex

@inline function vel_mag(u, equations::CompressibleEulerEquations3D)
rho, rho_v1, rho_v2, rho_v3, _ = u
return sqrt(rho_v1^2 + rho_v2^2 + rho_v3^2) / rho
end

volume_flux = flux_ranocha
solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs,
volume_integral = VolumeIntegralFluxDifferencing(volume_flux))

coordinates_min = (-1.0, -1.0, -1.0) .* pi
coordinates_max = (1.0, 1.0, 1.0) .* pi

trees_per_dimension = (2, 2, 2)

mesh = P4estMesh(trees_per_dimension, polydeg = 3,
coordinates_min = coordinates_min, coordinates_max = coordinates_max,
periodicity = (true, true, true), initial_refinement_level = 0)

semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic),
initial_condition, solver)

###############################################################################
# ODE solvers, callbacks etc.

tspan = (0.0, 0.5)
ode = semidiscretize(semi, tspan)

summary_callback = SummaryCallback()

analysis_interval = 50
analysis_callback = AnalysisCallback(semi, interval = analysis_interval,
save_analysis = true,
extra_analysis_integrals = (energy_kinetic,
energy_internal,
enstrophy))
save_solution = SaveSolutionCallback(interval = 100,
save_initial_solution = true,
save_final_solution = true,
solution_variables = cons2prim)

amr_indicator = IndicatorLöhner(semi, variable = vel_mag)

amr_controller = ControllerThreeLevel(semi, amr_indicator,
base_level = 0,
med_level = 1, med_threshold = 0.1,
max_level = 3, max_threshold = 0.2)

amr_callback = AMRCallback(semi, amr_controller,
interval = 5,
adapt_initial_condition = false,
adapt_initial_condition_only_refine = false)

alive_callback = AliveCallback(analysis_interval = analysis_interval)

callbacks = CallbackSet(summary_callback,
analysis_callback,
alive_callback,
amr_callback,
save_solution)

###############################################################################
# run the simulation

time_int_tol = 1e-8
sol = solve(ode, RDPK3SpFSAL49(); abstol = time_int_tol, reltol = time_int_tol,
ode_default_options()..., callback = callbacks)
summary_callback() # print the timer summary
4 changes: 2 additions & 2 deletions src/callbacks_step/amr_dg2d.jl
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@@ -137,7 +137,7 @@ function refine!(u_ode::AbstractVector, adaptor, mesh::Union{TreeMesh{2}, P4estM
end

function refine!(u_ode::AbstractVector, adaptor,
mesh::Union{TreeMesh{2}, P4estMesh{2}, TreeMesh{3}},
mesh::Union{TreeMesh{2}, P4estMesh{2}, TreeMesh{3}, P4estMesh{3}},
equations, dg::DGSEM, cache, cache_parabolic,
elements_to_refine)
# Call `refine!` for the hyperbolic part, which does the heavy lifting of
@@ -299,7 +299,7 @@ function coarsen!(u_ode::AbstractVector, adaptor,
end

function coarsen!(u_ode::AbstractVector, adaptor,
mesh::Union{TreeMesh{2}, P4estMesh{2}, TreeMesh{3}},
mesh::Union{TreeMesh{2}, P4estMesh{2}, TreeMesh{3}, P4estMesh{3}},
equations, dg::DGSEM, cache, cache_parabolic,
elements_to_remove)
# Call `coarsen!` for the hyperbolic part, which does the heavy lifting of
8 changes: 7 additions & 1 deletion src/callbacks_step/summary.jl
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@@ -152,7 +152,13 @@ function initialize_summary_callback(cb::DiscreteCallback, u, t, integrator;
Polyester.reset_threads!()
end

mpi_isroot() || return nothing
# The summary callback should only print information on the root process.
# However, all other MPI processes should also reset the timer so that
# it can be used to diagnose performance.
if !mpi_isroot()
reset_timer!(timer())
return nothing
end

print_startup_message()

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