format examples (#1531)

* format examples

* check formatting of examples in CI

* update style guide

* fix weird formatting

* fix formatting of binary operators

* format again

.github/workflows/FormatCheck.yml

@@ -30,7 +30,7 @@ jobs:
         #       format(".")
         run: |
           julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
-          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "test", "utils"])'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
       - name: Format check
         run: |
           julia -e '

docs/src/styleguide.md

@@ -17,11 +17,11 @@ conventions, we apply and enforce automated source code formatting
   * Maximum line length (strictly): **92**.
   * Functions that mutate their *input* are named with a trailing `!`.
   * Functions order their parameters [similar to Julia Base](https://docs.julialang.org/en/v1/manual/style-guide/#Write-functions-with-argument-ordering-similar-to-Julia-Base-1).
-    * The main modified argument comes first. For example, if the right-hand side `du` is modified, 
-      it should come first. If only the `cache` is modified, e.g., in `prolong2interfaces!` 
+    * The main modified argument comes first. For example, if the right-hand side `du` is modified,
+      it should come first. If only the `cache` is modified, e.g., in `prolong2interfaces!`
       and its siblings, put the `cache` first.
     * Otherwise, use the order `mesh, equations, solver, cache`.
-    * If something needs to be specified in more detail for dispatch, put the additional argument before the general one 
+    * If something needs to be specified in more detail for dispatch, put the additional argument before the general one
       that is specified in more detail. For example, we use `have_nonconservative_terms(equations), equations`
       and `dg.mortar, dg`.
   * Prefer `for i in ...` to `for i = ...` for better semantic clarity and greater flexibility.
@@ -55,7 +55,7 @@ julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
 ```
 You can then recursively format the core Julia files in the Trixi.jl repo by executing
 ```shell
-julia -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+julia -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
 ```
 from inside the Trixi.jl repository. For convenience, there is also a script you can
 directly run from your terminal shell, which will automatically install JuliaFormatter in a
@@ -67,12 +67,12 @@ You can get more information about using the convenience script by running it wi
 `--help`/`-h` flag.
 
 ### Checking formatting before committing
-It can be convenient to check the formatting of source code automatically before each commit. 
+It can be convenient to check the formatting of source code automatically before each commit.
 We use git-hooks for it and provide a `pre-commit` script in the `utils` folder. The script uses
-[JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) just like formatting script that 
-runs over the whole Trixi.jl directory. 
-You can copy the `pre-commit`-script into `.git/hooks/pre-commit` and it will check your formatting 
+[JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) just like formatting script that
+runs over the whole Trixi.jl directory.
+You can copy the `pre-commit`-script into `.git/hooks/pre-commit` and it will check your formatting
 before each commit. If errors are found the commit is aborted and you can add the corrections via
-```shell 
+```shell
 git add -p
 ```

examples/dgmulti_1d/elixir_advection_gauss_sbp.jl

@@ -23,8 +23,8 @@ dg = DGMulti(polydeg = 3,
 
 cells_per_dimension = (8,)
 mesh = DGMultiMesh(dg, cells_per_dimension,
-                   coordinates_min=(-1.0,), coordinates_max=(1.0,),
-                   periodicity=true)
+                   coordinates_min = (-1.0,), coordinates_max = (1.0,),
+                   periodicity = true)
 
 ###############################################################################
 #  setup the test problem (no source term needed for linear advection)
@@ -49,20 +49,19 @@ ode = semidiscretize(semi, tspan)
 summary_callback = SummaryCallback()
 
 # analyse the solution in regular intervals and prints the results
-analysis_callback = AnalysisCallback(semi, interval=100, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
 
 # handles the re-calculation of the maximum Δt after each time step
-stepsize_callback = StepsizeCallback(cfl=0.75)
+stepsize_callback = StepsizeCallback(cfl = 0.75)
 
 # collect all callbacks such that they can be passed to the ODE solver
 callbacks = CallbackSet(summary_callback, analysis_callback, stepsize_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt=1.0, save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 1.0, save_everystep = false, callback = callbacks);
 
 # Print the timer summary
 summary_callback()
-

examples/dgmulti_1d/elixir_euler_fdsbp_periodic.jl

@@ -2,17 +2,19 @@
 using Trixi, OrdinaryDiffEq
 
 dg = DGMulti(element_type = Line(),
-             approximation_type = periodic_derivative_operator(
-               derivative_order=1, accuracy_order=4, xmin=0.0, xmax=1.0, N=50),
+             approximation_type = periodic_derivative_operator(derivative_order = 1,
+                                                               accuracy_order = 4,
+                                                               xmin = 0.0, xmax = 1.0,
+                                                               N = 50),
              surface_flux = flux_hll,
              volume_integral = VolumeIntegralWeakForm())
 
 equations = CompressibleEulerEquations1D(1.4)
 initial_condition = initial_condition_convergence_test
 source_terms = source_terms_convergence_test
 
-mesh = DGMultiMesh(dg, coordinates_min=(-1.0,),
-                       coordinates_max=( 1.0,))
+mesh = DGMultiMesh(dg, coordinates_min = (-1.0,),
+                   coordinates_max = (1.0,))
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
                                     source_terms = source_terms)
@@ -21,15 +23,16 @@ tspan = (0.0, 0.4)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
-stepsize_callback = StepsizeCallback(cfl=1.0)
-callbacks = CallbackSet(summary_callback, alive_callback, stepsize_callback, analysis_callback)
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
+stepsize_callback = StepsizeCallback(cfl = 1.0)
+callbacks = CallbackSet(summary_callback, alive_callback, stepsize_callback,
+                        analysis_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt = 0.5 * estimate_dt(mesh, dg), save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 0.5 * estimate_dt(mesh, dg), save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary

examples/dgmulti_1d/elixir_euler_flux_diff.jl

@@ -13,25 +13,25 @@ source_terms = source_terms_convergence_test
 
 cells_per_dimension = (8,)
 mesh = DGMultiMesh(dg, cells_per_dimension,
-                   coordinates_min=(-1.0,), coordinates_max=(1.0,), periodicity=true)
+                   coordinates_min = (-1.0,), coordinates_max = (1.0,), periodicity = true)
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg;
-                                    source_terms=source_terms)
+                                    source_terms = source_terms)
 
 tspan = (0.0, 1.1)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
 callbacks = CallbackSet(summary_callback,
                         analysis_callback,
                         alive_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt = 0.5 * estimate_dt(mesh, dg), save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 0.5 * estimate_dt(mesh, dg), save_everystep = false, callback = callbacks);
 
 summary_callback() # print the timer summary

examples/dgmulti_2d/elixir_advection_diffusion.jl

@@ -11,48 +11,52 @@ initial_condition_zero(x, t, equations::LinearScalarAdvectionEquation2D) = SVect
 initial_condition = initial_condition_zero
 
 # tag different boundary segments
-left(x, tol=50*eps()) = abs(x[1] + 1) < tol
-right(x, tol=50*eps()) = abs(x[1] - 1) < tol
-bottom(x, tol=50*eps()) = abs(x[2] + 1) < tol
-top(x, tol=50*eps()) = abs(x[2] - 1) < tol
+left(x, tol = 50 * eps()) = abs(x[1] + 1) < tol
+right(x, tol = 50 * eps()) = abs(x[1] - 1) < tol
+bottom(x, tol = 50 * eps()) = abs(x[2] + 1) < tol
+top(x, tol = 50 * eps()) = abs(x[2] - 1) < tol
 is_on_boundary = Dict(:left => left, :right => right, :top => top, :bottom => bottom)
 
 cells_per_dimension = (16, 16)
 mesh = DGMultiMesh(dg, cells_per_dimension; is_on_boundary)
 
 # BC types
-boundary_condition_left = BoundaryConditionDirichlet((x, t, equations) -> SVector(1 + 0.1 * x[2]))
+boundary_condition_left = BoundaryConditionDirichlet((x, t, equations) -> SVector(1 +
+                                                                                  0.1 *
+                                                                                  x[2]))
 boundary_condition_zero = BoundaryConditionDirichlet((x, t, equations) -> SVector(0.0))
 boundary_condition_neumann_zero = BoundaryConditionNeumann((x, t, equations) -> SVector(0.0))
 
 # define inviscid boundary conditions
 boundary_conditions = (; :left => boundary_condition_left,
-                         :bottom => boundary_condition_zero,
-                         :top => boundary_condition_do_nothing,
-                         :right => boundary_condition_do_nothing)
+                       :bottom => boundary_condition_zero,
+                       :top => boundary_condition_do_nothing,
+                       :right => boundary_condition_do_nothing)
 
 # define viscous boundary conditions
 boundary_conditions_parabolic = (; :left => boundary_condition_left,
-                                   :bottom => boundary_condition_zero,
-                                   :top => boundary_condition_zero,
-                                   :right => boundary_condition_neumann_zero)
+                                 :bottom => boundary_condition_zero,
+                                 :top => boundary_condition_zero,
+                                 :right => boundary_condition_neumann_zero)
 
-semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, dg;
-                                             boundary_conditions=(boundary_conditions, boundary_conditions_parabolic))
+semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic),
+                                             initial_condition, dg;
+                                             boundary_conditions = (boundary_conditions,
+                                                                    boundary_conditions_parabolic))
 
 tspan = (0.0, 1.5)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
 callbacks = CallbackSet(summary_callback, alive_callback)
 
 ###############################################################################
 # run the simulation
 
 time_int_tol = 1e-6
-sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol,
-            ode_default_options()..., callback=callbacks)
+sol = solve(ode, RDPK3SpFSAL49(); abstol = time_int_tol, reltol = time_int_tol,
+            ode_default_options()..., callback = callbacks)
 summary_callback() # print the timer summary

examples/dgmulti_2d/elixir_advection_diffusion_nonperiodic.jl

@@ -16,61 +16,63 @@ equations_parabolic = LaplaceDiffusion2D(diffusivity(), equations)
 #   to numerical partial differential equations.
 #   [DOI](https://doi.org/10.1007/978-3-319-41640-3_6).
 function initial_condition_erikkson_johnson(x, t, equations)
-  l = 4
-  epsilon = diffusivity() # Note: this requires epsilon < 0.6 due to the 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)
+    l = 4
+    epsilon = diffusivity() # Note: this requires epsilon < 0.6 due to the 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_erikkson_johnson
 
 # tag different boundary segments
-left(x, tol=50*eps()) = abs(x[1] + 1) < tol
-right(x, tol=50*eps()) = abs(x[1]) < tol
-bottom(x, tol=50*eps()) = abs(x[2] + 0.5) < tol
-top(x, tol=50*eps()) = abs(x[2] - 0.5) < tol
-entire_boundary(x, tol=50*eps()) = true
+left(x, tol = 50 * eps()) = abs(x[1] + 1) < tol
+right(x, tol = 50 * eps()) = abs(x[1]) < tol
+bottom(x, tol = 50 * eps()) = abs(x[2] + 0.5) < tol
+top(x, tol = 50 * eps()) = abs(x[2] - 0.5) < tol
+entire_boundary(x, tol = 50 * eps()) = true
 is_on_boundary = Dict(:left => left, :right => right, :top => top, :bottom => bottom,
                       :entire_boundary => entire_boundary)
 
 cells_per_dimension = (16, 16)
 mesh = DGMultiMesh(dg, cells_per_dimension;
-                   coordinates_min=(-1.0, -0.5),
-                   coordinates_max=(0.0, 0.5),
+                   coordinates_min = (-1.0, -0.5),
+                   coordinates_max = (0.0, 0.5),
                    is_on_boundary)
 
 # BC types
 boundary_condition = BoundaryConditionDirichlet(initial_condition)
 
 # define inviscid boundary conditions, enforce "do nothing" boundary condition at the outflow
-boundary_conditions = (; :left   => boundary_condition,
-                         :top    => boundary_condition,
-                         :bottom => boundary_condition,
-                         :right  => boundary_condition_do_nothing)
+boundary_conditions = (; :left => boundary_condition,
+                       :top => boundary_condition,
+                       :bottom => boundary_condition,
+                       :right => boundary_condition_do_nothing)
 
 # define viscous boundary conditions
 boundary_conditions_parabolic = (; :entire_boundary => boundary_condition)
 
-semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, dg;
-                                             boundary_conditions=(boundary_conditions, boundary_conditions_parabolic))
+semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic),
+                                             initial_condition, dg;
+                                             boundary_conditions = (boundary_conditions,
+                                                                    boundary_conditions_parabolic))
 
 tspan = (0.0, 1.5)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
 callbacks = CallbackSet(summary_callback, alive_callback)
 
 ###############################################################################
 # 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)
+sol = solve(ode, RDPK3SpFSAL49(); abstol = time_int_tol, reltol = time_int_tol,
+            ode_default_options()..., callback = callbacks)
 summary_callback() # print the timer summary

examples/dgmulti_2d/elixir_advection_diffusion_periodic.jl

@@ -8,29 +8,29 @@ equations = LinearScalarAdvectionEquation2D(0.0, 0.0)
 equations_parabolic = LaplaceDiffusion2D(5.0e-1, equations)
 
 function initial_condition_sharp_gaussian(x, t, equations::LinearScalarAdvectionEquation2D)
-  return SVector(exp(-100 * (x[1]^2 + x[2]^2)))
+    return SVector(exp(-100 * (x[1]^2 + x[2]^2)))
 end
 initial_condition = initial_condition_sharp_gaussian
 
 cells_per_dimension = (16, 16)
-mesh = DGMultiMesh(dg, cells_per_dimension, periodicity=true)
+mesh = DGMultiMesh(dg, cells_per_dimension, periodicity = true)
 semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic),
                                              initial_condition, dg)
 
 tspan = (0.0, 0.1)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
 callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation
 
 time_int_tol = 1e-6
-sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol,
-            dt = time_int_tol, ode_default_options()..., callback=callbacks)
+sol = solve(ode, RDPK3SpFSAL49(); abstol = time_int_tol, reltol = time_int_tol,
+            dt = time_int_tol, ode_default_options()..., callback = callbacks)
 
 summary_callback() # print the timer summary