Merge branch 'main' into sc/mhd-treemesh-3d

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v3
       - name: Check spelling
-        uses: crate-ci/[email protected].1
+        uses: crate-ci/[email protected].10

Project.toml

@@ -1,7 +1,7 @@
 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 = "0.5.30-pre"
+version = "0.5.31-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"

docs/literate/src/files/shock_capturing.jl

@@ -48,7 +48,7 @@
 # with the total energy $\mathbb{E}=\max\big(\frac{m_N^2}{\sum_{j=0}^N m_j^2}, \frac{m_{N-1}^2}{\sum_{j=0}^{N-1} m_j^2}\big)$,
 # threshold $\mathbb{T}= 0.5 * 10^{-1.8*(N+1)^{1/4}}$ and parameter $s=ln\big(\frac{1-0.0001}{0.0001}\big)\approx 9.21024$.
 
-# For computational efficiency, $\alpha_{min}$ is introduced und used for
+# For computational efficiency, $\alpha_{min}$ is introduced and used for
 # ```math
 # \tilde{\alpha} = \begin{cases}
 # 0, & \text{if } \alpha<\alpha_{min}\\

examples/p4est_2d_dgsem/elixir_advection_diffusion_nonperiodic_curved.jl

@@ -0,0 +1,96 @@
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the linear advection-diffusion equation
+
+diffusivity() = 5.0e-2
+advection_velocity = (1.0, 0.0)
+equations = LinearScalarAdvectionEquation2D(advection_velocity)
+equations_parabolic = LaplaceDiffusion2D(diffusivity(), equations)
+
+# Example setup taken from
+# - Truman Ellis, Jesse Chan, and Leszek Demkowicz (2016).
+#   Robust DPG methods for transient convection-diffusion.
+#   In: Building bridges: connections and challenges in modern approaches
+#   to numerical partial differential equations.
+#   [DOI](https://doi.org/10.1007/978-3-319-41640-3_6).
+function initial_condition_eriksson_johnson(x, t, equations)
+  l = 4
+  epsilon = diffusivity() # TODO: this requires epsilon < .6 due to sqrt
+  lambda_1 = (-1 + sqrt(1 - 4 * epsilon * l)) / (-2 * epsilon)
+  lambda_2 = (-1 - sqrt(1 - 4 * epsilon * l)) / (-2 * epsilon)
+  r1 = (1 + sqrt(1 + 4 * pi^2 * epsilon^2)) / (2 * epsilon)
+  s1 = (1 - sqrt(1 + 4 * pi^2 * epsilon^2)) / (2 * epsilon)
+  u = exp(-l * t) * (exp(lambda_1 * x[1]) - exp(lambda_2 * x[1])) +
+      cos(pi * x[2]) * (exp(s1 * x[1]) - exp(r1 * x[1])) / (exp(-s1) - exp(-r1))
+  return SVector{1}(u)
+end
+initial_condition = initial_condition_eriksson_johnson
+
+boundary_conditions = Dict(:x_neg => BoundaryConditionDirichlet(initial_condition),
+                           :y_neg => BoundaryConditionDirichlet(initial_condition),
+                           :y_pos => BoundaryConditionDirichlet(initial_condition),
+                           :x_pos => boundary_condition_do_nothing)
+
+boundary_conditions_parabolic = Dict(:x_neg => BoundaryConditionDirichlet(initial_condition), 
+                                     :x_pos => BoundaryConditionDirichlet(initial_condition), 
+                                     :y_neg => BoundaryConditionDirichlet(initial_condition), 
+                                     :y_pos => BoundaryConditionDirichlet(initial_condition))
+
+# Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux
+solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs)
+
+coordinates_min = (-1.0, -0.5) 
+coordinates_max = ( 0.0,  0.5) 
+
+# This maps the domain [-1, 1]^2 to [-1, 0] x [-0.5, 0.5] while also 
+# introducing a curved warping to interior nodes. 
+function mapping(xi, eta)
+    x = xi  + 0.1 * sin(pi * xi) * sin(pi * eta)
+    y = eta + 0.1 * sin(pi * xi) * sin(pi * eta)
+    return SVector(0.5 * (1 + x) - 1, 0.5 * y)
+end 
+
+trees_per_dimension = (4, 4)
+mesh = P4estMesh(trees_per_dimension,
+                 polydeg=3, initial_refinement_level=2,
+                 mapping=mapping, periodicity=(false, false))
+
+# A semidiscretization collects data structures and functions for the spatial discretization
+semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, solver, 
+                                             boundary_conditions = (boundary_conditions, boundary_conditions_parabolic))
+
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+# Create ODE problem with time span `tspan`
+tspan = (0.0, 1.0)
+ode = semidiscretize(semi, tspan);
+
+# At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
+# and resets the timers
+summary_callback = SummaryCallback()
+
+# The AnalysisCallback allows to analyse the solution in regular intervals and prints the results
+analysis_interval = 100
+analysis_callback = AnalysisCallback(semi, interval=analysis_interval)
+
+# The AliveCallback prints short status information in regular intervals
+alive_callback = AliveCallback(analysis_interval=analysis_interval)
+
+# Create a CallbackSet to collect all callbacks such that they can be passed to the ODE solver
+callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
+
+
+###############################################################################
+# run the simulation
+
+# OrdinaryDiffEq's `solve` method evolves the solution in time and executes the passed callbacks
+time_int_tol = 1.0e-11
+sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol,
+            ode_default_options()..., callback=callbacks)
+
+# Print the timer summary
+summary_callback()

examples/p4est_2d_dgsem/elixir_euler_sedov.jl

@@ -11,7 +11,7 @@ equations = CompressibleEulerEquations2D(1.4)
     initial_condition_sedov_blast_wave(x, t, equations::CompressibleEulerEquations2D)
 
 The Sedov blast wave setup based on Flash
-- http://flash.uchicago.edu/site/flashcode/user_support/flash_ug_devel/node184.html#SECTION010114000000000000000
+- https://flash.rochester.edu/site/flashcode/user_support/flash_ug_devel/node187.html#SECTION010114000000000000000
 """
 function initial_condition_sedov_blast_wave(x, t, equations::CompressibleEulerEquations2D)
   # Set up polar coordinates
@@ -20,7 +20,7 @@ function initial_condition_sedov_blast_wave(x, t, equations::CompressibleEulerEq
   y_norm = x[2] - inicenter[2]
   r = sqrt(x_norm^2 + y_norm^2)
 
-  # Setup based on http://flash.uchicago.edu/site/flashcode/user_support/flash_ug_devel/node184.html#SECTION010114000000000000000
+  # Setup based on https://flash.rochester.edu/site/flashcode/user_support/flash_ug_devel/node187.html#SECTION010114000000000000000
   r0 = 0.21875 # = 3.5 * smallest dx (for domain length=4 and max-ref=6)
   E = 1.0
   p0_inner = 3 * (equations.gamma - 1) * E / (3 * pi * r0^2)

examples/p4est_2d_dgsem/elixir_navierstokes_convergence.jl

@@ -0,0 +1,209 @@
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the ideal compressible Navier-Stokes equations
+
+prandtl_number() = 0.72
+mu() = 0.01
+
+equations = CompressibleEulerEquations2D(1.4)
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu=mu(), Prandtl=prandtl_number(),
+                                                          gradient_variables=GradientVariablesPrimitive())
+
+# Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux
+solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs,
+               volume_integral=VolumeIntegralWeakForm())
+
+coordinates_min = (-1.0, -1.0) # minimum coordinates (min(x), min(y))
+coordinates_max = ( 1.0,  1.0) # maximum coordinates (max(x), max(y))
+
+trees_per_dimension = (4, 4)
+mesh = P4estMesh(trees_per_dimension,
+                 polydeg=3, initial_refinement_level=2,
+                 coordinates_min=coordinates_min, coordinates_max=coordinates_max,
+                 periodicity=(true, false))
+
+# Note: the initial condition cannot be specialized to `CompressibleNavierStokesDiffusion2D`
+#       since it is called by both the parabolic solver (which passes in `CompressibleNavierStokesDiffusion2D`)
+#       and by the initial condition (which passes in `CompressibleEulerEquations2D`).
+# This convergence test setup was originally derived by Andrew Winters (@andrewwinters5000)
+function initial_condition_navier_stokes_convergence_test(x, t, equations)
+  # Amplitude and shift
+  A = 0.5
+  c = 2.0
+
+  # convenience values for trig. functions
+  pi_x = pi * x[1]
+  pi_y = pi * x[2]
+  pi_t = pi * t
+
+  rho = c + A * sin(pi_x) * cos(pi_y) * cos(pi_t)
+  v1  = sin(pi_x) * log(x[2] + 2.0) * (1.0 - exp(-A * (x[2] - 1.0)) ) * cos(pi_t)
+  v2  = v1
+  p   = rho^2
+
+  return prim2cons(SVector(rho, v1, v2, p), equations)
+end
+
+@inline function source_terms_navier_stokes_convergence_test(u, x, t, equations)
+  y = x[2]
+
+  # TODO: parabolic
+  # we currently need to hardcode these parameters until we fix the "combined equation" issue
+  # see also https://github.com/trixi-framework/Trixi.jl/pull/1160
+  inv_gamma_minus_one = inv(equations.gamma - 1)
+  Pr = prandtl_number()
+  mu_ = mu()
+
+  # Same settings as in `initial_condition`
+  # Amplitude and shift
+  A = 0.5
+  c = 2.0
+
+  # convenience values for trig. functions
+  pi_x = pi * x[1]
+  pi_y = pi * x[2]
+  pi_t = pi * t
+
+  # compute the manufactured solution and all necessary derivatives
+  rho    =  c  + A * sin(pi_x) * cos(pi_y) * cos(pi_t)
+  rho_t  = -pi * A * sin(pi_x) * cos(pi_y) * sin(pi_t)
+  rho_x  =  pi * A * cos(pi_x) * cos(pi_y) * cos(pi_t)
+  rho_y  = -pi * A * sin(pi_x) * sin(pi_y) * cos(pi_t)
+  rho_xx = -pi * pi * A * sin(pi_x) * cos(pi_y) * cos(pi_t)
+  rho_yy = -pi * pi * A * sin(pi_x) * cos(pi_y) * cos(pi_t)
+
+  v1    =       sin(pi_x) * log(y + 2.0) * (1.0 - exp(-A * (y - 1.0))) * cos(pi_t)
+  v1_t  = -pi * sin(pi_x) * log(y + 2.0) * (1.0 - exp(-A * (y - 1.0))) * sin(pi_t)
+  v1_x  =  pi * cos(pi_x) * log(y + 2.0) * (1.0 - exp(-A * (y - 1.0))) * cos(pi_t)
+  v1_y  =       sin(pi_x) * (A * log(y + 2.0) * exp(-A * (y - 1.0)) + (1.0 - exp(-A * (y - 1.0))) / (y + 2.0)) * cos(pi_t)
+  v1_xx = -pi * pi * sin(pi_x) * log(y + 2.0) * (1.0 - exp(-A * (y - 1.0))) * cos(pi_t)
+  v1_xy =  pi * cos(pi_x) * (A * log(y + 2.0) * exp(-A * (y - 1.0)) + (1.0 - exp(-A * (y - 1.0))) / (y + 2.0)) * cos(pi_t)
+  v1_yy = (sin(pi_x) * ( 2.0 * A * exp(-A * (y - 1.0)) / (y + 2.0)
+                         - A * A * log(y + 2.0) * exp(-A * (y - 1.0))
+                         - (1.0 - exp(-A * (y - 1.0))) / ((y + 2.0) * (y + 2.0))) * cos(pi_t))
+  v2    = v1
+  v2_t  = v1_t
+  v2_x  = v1_x
+  v2_y  = v1_y
+  v2_xx = v1_xx
+  v2_xy = v1_xy
+  v2_yy = v1_yy
+
+  p    = rho * rho
+  p_t  = 2.0 * rho * rho_t
+  p_x  = 2.0 * rho * rho_x
+  p_y  = 2.0 * rho * rho_y
+  p_xx = 2.0 * rho * rho_xx + 2.0 * rho_x * rho_x
+  p_yy = 2.0 * rho * rho_yy + 2.0 * rho_y * rho_y
+
+  # Note this simplifies slightly because the ansatz assumes that v1 = v2
+  E   = p * inv_gamma_minus_one + 0.5 * rho * (v1^2 + v2^2)
+  E_t = p_t * inv_gamma_minus_one + rho_t * v1^2 + 2.0 * rho * v1 * v1_t
+  E_x = p_x * inv_gamma_minus_one + rho_x * v1^2 + 2.0 * rho * v1 * v1_x
+  E_y = p_y * inv_gamma_minus_one + rho_y * v1^2 + 2.0 * rho * v1 * v1_y
+
+  # Some convenience constants
+  T_const = equations.gamma * inv_gamma_minus_one / Pr
+  inv_rho_cubed = 1.0 / (rho^3)
+
+  # compute the source terms
+  # density equation
+  du1 = rho_t + rho_x * v1 + rho * v1_x + rho_y * v2 + rho * v2_y
+
+  # x-momentum equation
+  du2 = ( rho_t * v1 + rho * v1_t + p_x + rho_x * v1^2
+                                        + 2.0   * rho  * v1 * v1_x
+                                        + rho_y * v1   * v2
+                                        + rho   * v1_y * v2
+                                        + rho   * v1   * v2_y
+    # stress tensor from x-direction
+                      - 4.0 / 3.0 * v1_xx * mu_
+                      + 2.0 / 3.0 * v2_xy * mu_
+                      - v1_yy             * mu_
+                      - v2_xy             * mu_ )
+  # y-momentum equation
+  du3 = ( rho_t * v2 + rho * v2_t + p_y + rho_x * v1    * v2
+                                        + rho   * v1_x  * v2
+                                        + rho   * v1    * v2_x
+                                        +         rho_y * v2^2
+                                        + 2.0   * rho   * v2 * v2_y
+    # stress tensor from y-direction
+                      - v1_xy             * mu_
+                      - v2_xx             * mu_
+                      - 4.0 / 3.0 * v2_yy * mu_
+                      + 2.0 / 3.0 * v1_xy * mu_ )
+  # total energy equation
+  du4 = ( E_t + v1_x * (E + p) + v1 * (E_x + p_x)
+              + v2_y * (E + p) + v2 * (E_y + p_y)
+    # stress tensor and temperature gradient terms from x-direction
+                                - 4.0 / 3.0 * v1_xx * v1   * mu_
+                                + 2.0 / 3.0 * v2_xy * v1   * mu_
+                                - 4.0 / 3.0 * v1_x  * v1_x * mu_
+                                + 2.0 / 3.0 * v2_y  * v1_x * mu_
+                                - v1_xy     * v2           * mu_
+                                - v2_xx     * v2           * mu_
+                                - v1_y      * v2_x         * mu_
+                                - v2_x      * v2_x         * mu_
+         - T_const * inv_rho_cubed * (        p_xx * rho   * rho
+                                      - 2.0 * p_x  * rho   * rho_x
+                                      + 2.0 * p    * rho_x * rho_x
+                                      -       p    * rho   * rho_xx ) * mu_
+    # stress tensor and temperature gradient terms from y-direction
+                                - v1_yy     * v1           * mu_
+                                - v2_xy     * v1           * mu_
+                                - v1_y      * v1_y         * mu_
+                                - v2_x      * v1_y         * mu_
+                                - 4.0 / 3.0 * v2_yy * v2   * mu_
+                                + 2.0 / 3.0 * v1_xy * v2   * mu_
+                                - 4.0 / 3.0 * v2_y  * v2_y * mu_
+                                + 2.0 / 3.0 * v1_x  * v2_y * mu_
+         - T_const * inv_rho_cubed * (        p_yy * rho   * rho
+                                      - 2.0 * p_y  * rho   * rho_y
+                                      + 2.0 * p    * rho_y * rho_y
+                                      -       p    * rho   * rho_yy ) * mu_ )
+
+  return SVector(du1, du2, du3, du4)
+end
+
+initial_condition = initial_condition_navier_stokes_convergence_test
+
+# BC types
+velocity_bc_top_bottom = NoSlip((x, t, equations) -> initial_condition_navier_stokes_convergence_test(x, t, equations)[2:3])
+heat_bc_top_bottom = Adiabatic((x, t, equations) -> 0.0)
+boundary_condition_top_bottom = BoundaryConditionNavierStokesWall(velocity_bc_top_bottom, heat_bc_top_bottom)
+
+# define inviscid boundary conditions
+boundary_conditions = Dict(:y_neg => boundary_condition_slip_wall,
+                           :y_pos => boundary_condition_slip_wall)
+
+# define viscous boundary conditions
+boundary_conditions_parabolic = Dict(:y_neg => boundary_condition_top_bottom,
+                                     :y_pos => boundary_condition_top_bottom)
+
+semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, solver;
+                                             boundary_conditions=(boundary_conditions, boundary_conditions_parabolic),
+                                             source_terms=source_terms_navier_stokes_convergence_test)
+
+# ###############################################################################
+# # ODE solvers, callbacks etc.
+
+# Create ODE problem with time span `tspan`
+tspan = (0.0, 0.5)
+ode = semidiscretize(semi, tspan)
+
+summary_callback = SummaryCallback()
+alive_callback = AliveCallback(alive_interval=10)
+analysis_interval = 100
+analysis_callback = AnalysisCallback(semi, interval=analysis_interval)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
+
+###############################################################################
+# run the simulation
+
+time_int_tol = 1e-8
+sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol, dt = 1e-5,
+            ode_default_options()..., callback=callbacks)
+summary_callback() # print the timer summary
+