remove restriction of DiffEqBase.jl (used as hotfix) (#2264)

* remove restriction of DiffEqBase.jl (used as hotfix)

* ODE_DEFAULT_NORM moved

* use ADTypes

* fix another depwarn

* bump DiffEqCallbacks

* format

* allow older version of ADTypes

* Update test/Project.toml

Co-authored-by: Joshua Lampert <[email protected]>

* restrict to ADTypes v1

* bump ADTypes for NonlinearSolve.jl

* fix compat bounds for Downgrade action

* fix Aqua.jl issue

* add DiffEqBase extension to fix callback issues with custom integrators

* ignore several run folders

* sort alphabetically

* format

* import fix

* allow v3 of DiffEqCallbacks

* require Static.jl v1 for DiffEqBase.jl v6.154 (required for new DiffEqCallbacks stuff)

* require StaticArrayInterface 1.5.1 for Static.jl v1

* fix Aqua tests

* fix test values

* fix restart_file

* require Octavian.jl v0.3.28 for Static.jl

* require LoopVectorization.jl v0.12.171 for Static.jl

* require StrideArrays.jl v0.1.29 for Static.jl

* require Polyester.jl v0.7.15 for Static.jl

* fix typo

* require OrdinaryDiffEq.jl v6.88 for FastBroadcast.jl version required by Static.jl v1

* require Polyester.jl v0.7.16 for OrdinaryDiffEqPRK.jl

* require MuladdMacro v0.2.4 for OrdinaryDiffEqPRK.jl

* require Static.jl v1.1.1 for OrdinaryDiffEqHighOrderRK.jl

* require ADTypes.jl v1.7.1 for OrdinaryDiffEqNonlinearSolve.jl

* fix documentation about PERK methods

* fix some more test values and tolerances

* remove extras that are not required anymore since Julia v1.9

* make DiffEqBase a regular dep instead of a weakdep

Trixi.jl depends on DiffEqBase.jl already via DiffEqCallbacks.jl. Making DiffEqBase.jl
a regular dep instead of a weakdep fixes a cyclic dependency issue with extensions.

* format

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* add NLsolve to docs/Project.toml

---------

Co-authored-by: Joshua Lampert <[email protected]>
Co-authored-by: Joshua Lampert <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: 3 people

.github/workflows/Downgrade.yml

@@ -72,7 +72,7 @@ jobs:
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-downgrade-compat@v1
         with:
-          skip: LinearAlgebra,Printf,SparseArrays,UUIDs,DiffEqBase,DelimitedFiles,Test,Downloads,Random
+          skip: LinearAlgebra,Printf,SparseArrays,UUIDs,DelimitedFiles,Test,Downloads,Random
           projects: ., test
       - uses: julia-actions/julia-buildpkg@v1
         env:

.gitignore

@@ -28,7 +28,7 @@ coverage_report/
 
 .DS_Store
 
-run
-run/*
+run*/
+run*/*
 
 LocalPreferences.toml

Project.toml

@@ -69,54 +69,48 @@ ConstructionBase = "1.5"
 Convex = "0.16"
 DataStructures = "0.18.15"
 DelimitedFiles = "1"
-DiffEqBase = "6 - 6.143"
-DiffEqCallbacks = "2.35"
+DiffEqBase = "6.154"
+DiffEqCallbacks = "2.35, 3, 4"
 Downloads = "1.6"
 ECOS = "1.1.2"
 EllipsisNotation = "1.0"
 FillArrays = "1.9"
-ForwardDiff = "0.10.24"
+ForwardDiff = "0.10.36"
 HDF5 = "0.16.10, 0.17"
 LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
-LoopVectorization = "0.12.151"
+LoopVectorization = "0.12.171"
 MPI = "0.20.6"
 Makie = "0.21, 0.22"
-MuladdMacro = "0.2.2"
+MuladdMacro = "0.2.4"
 NLsolve = "4.5.1"
-Octavian = "0.3.21"
+Octavian = "0.3.28"
 OffsetArrays = "1.13"
 P4est = "0.4.12"
-Polyester = "0.7.10"
+Polyester = "0.7.16"
 PrecompileTools = "1.2"
-Preferences = "1.3"
+Preferences = "1.4"
 Printf = "1"
 RecipesBase = "1.3.4"
 RecursiveArrayTools = "3.29"
-Reexport = "1.0"
+Reexport = "1.2"
 Requires = "1.1"
 SciMLBase = "2.67.0"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
 StableRNGs = "1.0.2"
 StartUpDG = "1.1.5"
-Static = "0.8.7, 1"
-StaticArrayInterface = "1.4"
-StaticArrays = "1.7"
-StrideArrays = "0.1.26"
+Static = "1.1.1"
+StaticArrayInterface = "1.5.1"
+StaticArrays = "1.9"
+StrideArrays = "0.1.29"
 StructArrays = "0.6.18"
 SummationByPartsOperators = "0.5.52"
 T8code = "0.7.4"
-TimerOutputs = "0.5.7"
+TimerOutputs = "0.5.23"
 Triangulate = "2.2"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
 TrixiBase = "0.1.3"
 UUIDs = "1.6"
 julia = "1.10"
-
-[extras]
-Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
-ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
-Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"

docs/Project.toml

@@ -9,6 +9,7 @@ HOHQMesh = "e4f4c7b8-17cb-445a-93c5-f69190ed6c8c"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -26,6 +27,7 @@ HOHQMesh = "0.1, 0.2"
 LaTeXStrings = "1.2"
 Literate = "2.9"
 Measurements = "2.5"
+NLsolve = "4.5.1"
 OrdinaryDiffEq = "6.49.1"
 Plots = "1.9"
 Test = "1"

docs/src/time_integration.md

@@ -13,7 +13,7 @@ Some common options for `solve` from [OrdinaryDiffEq.jl](https://github.com/SciM
 are the following. Further documentation can be found in the
 [SciML docs](https://diffeq.sciml.ai/v6.8/basics/common_solver_opts/).
 - If you use a fixed time step method like `CarpenterKennedy2N54`, you need to pass
-  a time step as `dt=...`. If you use a [`StepsizeCallback`](@ref), the value passed 
+  a time step as `dt=...`. If you use a [`StepsizeCallback`](@ref), the value passed
   as `dt=...` is irrelevant since it will be overwritten by the [`StepsizeCallback`](@ref).
   If you want to use an adaptive time step method such as `SSPRK43` or `RDPK3SpFSAL49`
   and still want to use CFL-based step size control via the [`StepsizeCallback`](@ref),
@@ -25,12 +25,12 @@ are the following. Further documentation can be found in the
 - SSP methods and many low-storage methods from OrdinaryDiffEq.jl support
   `stage_limiter!`s and `step_limiter!`s, e.g., [`PositivityPreservingLimiterZhangShu`](@ref) and [`EntropyBoundedLimiter`](@ref)
   from Trixi.jl.
-- If you start Julia with multiple threads and want to use them also in the time 
+- If you start Julia with multiple threads and want to use them also in the time
   integration method from OrdinaryDiffEq.jl, you need to pass the keyword argument
-  `thread=OrdinaryDiffEq.True()` to the algorithm, e.g., 
-  `RDPK3SpFSAL49(thread=OrdinaryDiffEq.True())` or 
+  `thread=OrdinaryDiffEq.True()` to the algorithm, e.g.,
+  `RDPK3SpFSAL49(thread=OrdinaryDiffEq.True())` or
   `CarpenterKennedy2N54(thread=OrdinaryDiffEq.True(), williamson_condition=false)`.
-  For more information on using thread-based parallelism in Trixi.jl, please refer to 
+  For more information on using thread-based parallelism in Trixi.jl, please refer to
   [Shared-memory parallelization with threads](@ref).
 - If you use error-based step size control (see also the section on
   [error-based adaptive step sizes](@ref adaptive_step_sizes)) together with MPI, you need to
@@ -50,7 +50,7 @@ are the following. Further documentation can be found in the
 ### Stabilized Explicit Runge-Kutta Methods
 
 Optimized explicit schemes aim to maximize the timestep $\Delta t$ for a given simulation setup.
-Formally, this boils down to an optimization problem of the form 
+Formally, this boils down to an optimization problem of the form
 ```math
 \underset{P_{p;S} \, \in \, \mathcal{P}_{p;S}}{\max} \Delta t \text{ such that } \big \vert P_{p;S}(\Delta t \lambda_m) \big \vert \leq 1, \quad  m = 1 , \dots , M \tag{1}
 ```
@@ -79,12 +79,12 @@ Nevertheless, due to their optimized stability properties and low-storage nature
 
 #### Tutorial: Using `PairedExplicitRK2`
 
-In this tutorial, we will demonstrate how you can use the second-order PERK time integrator. You need the packages `Convex.jl` and `ECOS.jl`, so be sure they are added to your environment.
+In this tutorial, we will demonstrate how you can use the second-order PERK time integrator. You need the packages `Convex.jl`, `ECOS.jl`, and `NLsolve.jl`, so be sure they are added to your environment.
 
 First, you need to load the necessary packages:
 
 ```@example PERK-example-1
-using Convex, ECOS
+using Convex, ECOS, NLsolve
 using OrdinaryDiffEq
 using Trixi
 ```
@@ -96,7 +96,7 @@ Then, define the ODE problem and the semidiscretization setup. For this example,
 cells_per_dimension = 100
 coordinates_min = 0.0
 coordinates_max = 1.0
-mesh = StructuredMesh(cells_per_dimension, 
+mesh = StructuredMesh(cells_per_dimension,
                       coordinates_min, coordinates_max)
 
 # Define the equation and initial condition
@@ -109,8 +109,8 @@ initial_condition = initial_condition_convergence_test
 solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
 # Define the semidiscretization
-semi = SemidiscretizationHyperbolic(mesh, 
-                                    equations, initial_condition, 
+semi = SemidiscretizationHyperbolic(mesh,
+                                    equations, initial_condition,
                                     solver)
 ```
 
@@ -125,14 +125,14 @@ analysis_callback = AnalysisCallback(semi, interval = 200)
 stepsize_callback = StepsizeCallback(cfl = 2.5)
 
 # Create a CallbackSet to collect all callbacks
-callbacks = CallbackSet(summary_callback, 
-                        alive_callback, 
-                        analysis_callback, 
+callbacks = CallbackSet(summary_callback,
+                        alive_callback,
+                        analysis_callback,
                         stepsize_callback)
 ```
 
-Now, we define the ODE problem by specifying the time span over which the ODE will be solved. 
-The `tspan` parameter is a tuple `(t_start, t_end)` that defines the start and end times for the simulation. 
+Now, we define the ODE problem by specifying the time span over which the ODE will be solved.
+The `tspan` parameter is a tuple `(t_start, t_end)` that defines the start and end times for the simulation.
 The `semidiscretize` function is used to create the ODE problem from the simulation setup.
 
 ```@example PERK-example-1
@@ -145,10 +145,10 @@ ode = semidiscretize(semi, tspan)
 
 Next, we will construct the time integrator. In order to do this, you need the following components:
 
-  - Number of stages: The number of stages $S$ in the Runge-Kutta method. 
+  - Number of stages: The number of stages $S$ in the Runge-Kutta method.
   In this example, we use `6` stages.
-  - Time span (`tspan`): A tuple `(t_start, t_end)` that defines the time span over which the ODE will be solved. 
-  This defines the bounds for the bisection routine for the optimal timestep $\Delta t$ used in calculating the polynomial coefficients at optimization stage. 
+  - Time span (`tspan`): A tuple `(t_start, t_end)` that defines the time span over which the ODE will be solved.
+  This defines the bounds for the bisection routine for the optimal timestep $\Delta t$ used in calculating the polynomial coefficients at optimization stage.
   This variable is already defined in step 5.
   - Semidiscretization (`semi`): The semidiscretization setup that includes the mesh, equations, initial condition, and solver. In this example, this variable is already defined in step 3.
   In the background, we compute from `semi` the Jacobian $J$ evaluated at the initial condition using [`jacobian_ad_forward`](https://trixi-framework.github.io/Trixi.jl/stable/reference-trixi/#Trixi.jacobian_ad_forward-Tuple{Trixi.AbstractSemidiscretization}).
@@ -182,9 +182,9 @@ There are two additional constructors for the `PairedExplicitRK2` method besides
 
 In the previous tutorial the CFL number was set manually to $2.5$.
 To avoid the manual trial-and-error process behind this, instantiations of `AbstractPairedExplicitRK` methods can automatically compute the stable CFL number for a given simulation setup using the [`Trixi.calculate_cfl`](@ref) function.
-When constructing the time integrator from a semidiscretization `semi`, 
+When constructing the time integrator from a semidiscretization `semi`,
 ```@example PERK-example-1
-# Construct third-order paired-explicit Runge-Kutta method with 8 stages for given simulation setup.                               
+# Construct third-order paired-explicit Runge-Kutta method with 8 stages for given simulation setup.
 ode_algorithm = Trixi.PairedExplicitRK3(8, tspan, semi)
 ```
 the maximum timestep `dt` is stored by the `ode_algorithm`.

examples/tree_1d_dgsem/elixir_advection_diffusion.jl

@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEq, ADTypes
 using Trixi
 
 ###############################################################################
@@ -87,7 +87,8 @@ callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, sav
 # OrdinaryDiffEq's `solve` method evolves the solution in time and executes the passed callbacks
 time_int_tol = 1.0e-10
 time_abs_tol = 1.0e-10
-sol = solve(ode, KenCarp4(autodiff = false), abstol = time_abs_tol, reltol = time_int_tol,
+sol = solve(ode, KenCarp4(autodiff = AutoFiniteDiff()),
+            abstol = time_abs_tol, reltol = time_int_tol,
             save_everystep = false, callback = callbacks)
 
 # Print the timer summary

examples/tree_1d_dgsem/elixir_advection_diffusion_restart.jl

@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEq, ADTypes
 using Trixi
 
 ###############################################################################
@@ -10,7 +10,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))
 ###############################################################################
 # initialize the ODE
 
-restart_file = "restart_000000018.h5"
+restart_file = "restart_000000012.h5"
 restart_filename = joinpath("out", restart_file)
 tspan = (load_time(restart_filename), 2.0)
 
@@ -22,7 +22,8 @@ callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, KenCarp4(autodiff = false), abstol = time_abs_tol, reltol = time_int_tol,
+sol = solve(ode, KenCarp4(autodiff = AutoFiniteDiff()),
+            abstol = time_abs_tol, reltol = time_int_tol,
             save_everystep = false, callback = callbacks)
 
 # Print the timer summary

examples/tree_3d_dgsem/elixir_lbm_taylor_green_vortex.jl

@@ -73,5 +73,5 @@ callbacks = CallbackSet(summary_callback,
 sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             save_everystep = false, callback = callbacks,
-            save_start = false, alias_u0 = true);
+            save_start = false, alias = ODEAliasSpecifier(alias_u0 = true));
 summary_callback() # print the timer summary

src/Trixi.jl

@@ -45,6 +45,7 @@ using DelimitedFiles: readdlm
 using Downloads: Downloads
 using CodeTracking: CodeTracking
 using ConstructionBase: ConstructionBase
+using DiffEqBase: DiffEqBase, get_tstops, get_tstops_array
 using DiffEqCallbacks: PeriodicCallback, PeriodicCallbackAffect
 @reexport using EllipsisNotation # ..
 using FillArrays: Ones, Zeros

src/time_integration/methods_2N.jl

@@ -14,7 +14,7 @@ abstract type SimpleAlgorithm2N end
 The following structures and methods provide a minimal implementation of
 the low-storage explicit Runge-Kutta method of
 
-- Carpenter, Kennedy (1994) 
+- Carpenter, Kennedy (1994)
   Fourth-order 2N-storage Runge-Kutta schemes (Solution 3)
   URL: https://ntrs.nasa.gov/citations/19940028444
   File: https://ntrs.nasa.gov/api/citations/19940028444/downloads/19940028444.pdf
@@ -53,7 +53,7 @@ end
 The following structures and methods provide a minimal implementation of
 the low-storage explicit Runge-Kutta method of
 
-- Carpenter, Kennedy (1994) 
+- Carpenter, Kennedy (1994)
   Third-order 2N-storage Runge-Kutta schemes with error control
   URL: https://ntrs.nasa.gov/citations/19940028444
   File: https://ntrs.nasa.gov/api/citations/19940028444/downloads/19940028444.pdf
@@ -91,7 +91,7 @@ end
 # https://diffeq.sciml.ai/v6.8/basics/integrator/#Handing-Integrators-1
 # which are used in Trixi.jl.
 mutable struct SimpleIntegrator2N{RealT <: Real, uType, Params, Sol, F, Alg,
-                                  SimpleIntegrator2NOptions}
+                                  SimpleIntegrator2NOptions} <: AbstractTimeIntegrator
     u::uType #
     du::uType
     u_tmp::uType
@@ -232,7 +232,7 @@ function set_proposed_dt!(integrator::SimpleIntegrator2N, dt)
     integrator.dt = dt
 end
 
-# Required e.g. for `glm_speed_callback` 
+# Required e.g. for `glm_speed_callback`
 function get_proposed_dt(integrator::SimpleIntegrator2N)
     return integrator.dt
 end