Merge branch 'main' into dg_gpu_port

.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].6

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/src/github-git.md

@@ -112,7 +112,7 @@ branch, and the corresponding pull request will be updated automatically.
 Please note that a review has nothing to do with the lack of experience of the
 person developing changes: We try to review all code before it gets added to
 `main`, even from the most experienced developers. This is good practice and
-helps to keep the error rate low while ensuring the the code is developed in a
+helps to keep the error rate low while ensuring that the code is developed in a
 consistent fashion. Furthermore, do not take criticism of your code personally -
 we just try to keep Trixi.jl as accessible and easy to use for everyone.
 
@@ -121,7 +121,7 @@ Once your branch is reviewed and declared ready for merging by the reviewer,
 make sure that all the latest changes have been pushed. Then, one of the
 developers will merge your PR. If you are one of the developers, you can also go
 to the pull request page on GitHub and and click on **Merge pull request**.
-Voilá, you are done! Your branch will have been merged to
+Voilà, you are done! Your branch will have been merged to
 `main` and the source branch will have been deleted in the GitHub repository
 (if you are not working in your own fork).
 

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
+