Merge branch 'main' into LinEuler1D

CONTRIBUTING.md

@@ -1,9 +1,12 @@
 # Contributing
 
 Trixi.jl is an open-source project and we are very happy to accept contributions
-from the community. Please feel free to open issues or submit patches (preferably
-as pull requests) any time. For planned larger contributions, it is often
-beneficial to get in contact with one of the principal developers first (see
+from the community. Please feel free to
+[open issues](https://github.com/trixi-framework/Trixi.jl/issues/new/choose)
+or submit patches (preferably as
+[pull requests](https://github.com/trixi-framework/Trixi.jl/pulls))
+any time. For planned larger contributions, it is often beneficial to get
+in contact with one of the principal developers first (see
 [AUTHORS.md](AUTHORS.md)).
 
 Trixi.jl and its contributions are licensed under the MIT license (see

NEWS.md

@@ -4,13 +4,20 @@ 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 v0.7 lifecycle
+
+#### Added
+- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension
+  to 1D and 3D on `TreeMesh`.
+
+
 ## Changes when updating to v0.7 from v0.6.x
 
 #### Added
 
 #### Changed
 
-- The default wave speed estimate used within `flux_hll` is now `min_max_speed_davis` 
+- The default wave speed estimate used within `flux_hll` is now `min_max_speed_davis`
   instead of `min_max_speed_naive`.
 
 #### Deprecated
@@ -26,7 +33,7 @@ for human readability.
 #### Added
 - AMR for hyperbolic-parabolic equations on 3D `P4estMesh`
 - `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D`
-- Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, 
+- Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh,
   can now be digested by Trixi in 2D and 3D.
 - Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh`
 - Added Lighthill-Whitham-Richards (LWR) traffic model
@@ -40,7 +47,7 @@ for human readability.
 #### Changed
 
 - The wave speed estimates for `flux_hll`, `FluxHLL()` are now consistent across equations.
-  In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now 
+  In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now
   conceptually identical across equations.
   Users, who have been using `flux_hll` for MHD have now to use `flux_hlle` in order to use the
   Einfeldt wave speed estimate.

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 = "0.7.3-pre"
+version = "0.7.5-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -31,7 +31,6 @@ RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StartUpDG = "472ebc20-7c99-4d4b-9470-8fde4e9faa0f"
@@ -84,7 +83,6 @@ RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
 SciMLBase = "1.90, 2"
-Setfield = "1"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
 StartUpDG = "0.17.7"

README.md

@@ -10,7 +10,8 @@
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
-[![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Trixi)](https://pkgs.genieframework.com?packages=Trixi)
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8695/badge)](https://www.bestpractices.dev/projects/8695)
+<!-- [![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Trixi)](https://pkgs.genieframework.com?packages=Trixi) -->
 <!-- [![GitHub commits since tagged version](https://img.shields.io/github/commits-since/trixi-framework/Trixi.jl/v0.3.43.svg?style=social&logo=github)](https://github.com/trixi-framework/Trixi.jl) -->
 <!-- [![PkgEval](https://juliaci.github.io/NanosoldierReports/pkgeval_badges/T/Trixi.svg)](https://juliaci.github.io/NanosoldierReports/pkgeval_badges/report.html) -->
 

SECURITY.md

@@ -0,0 +1,30 @@
+# Security Policy
+
+The Trixi.jl development team takes security issues seriously. We appreciate
+all efforts to responsibly disclose any security issues and will make every
+effort to acknowledge contributions.
+
+
+## Supported Versions
+
+The current stable release following the interpretation of
+[semantic versioning (SemVer)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
+used in the Julia ecosystem is supported with security updates.
+
+
+## Reporting a Vulnerability
+
+To report a security issue, please use the GitHub Security Advisory
+["Report a Vulnerability"](https://github.com/trixi-framework/Trixi.jl/security/advisories/new)
+tab.
+
+We will send a response indicating the next steps in handling your report.
+After the initial reply to your report, we will keep you informed of the
+progress towards a fix and full announcement, and may ask for additional
+information or guidance.
+
+Please report security bugs in third-party modules directly to the person
+or team maintaining the module.
+
+Public notifications of vulnerabilities will be shared in community channels
+such as Slack.

docs/.gitignore

@@ -1 +1,3 @@
 src/code_of_conduct.md
+src/contributing.md
+

docs/literate/src/files/scalar_linear_advection_1d.jl

@@ -115,7 +115,7 @@ integral = sum(nodes.^3 .* weights)
 # To approximate the solution, we need to get the polynomial coefficients $\{u_j^{Q_l}\}_{j=0}^N$
 # for every element $Q_l$.
 
-# After defining all nodes, we can implement the spatial coordinate $x$ and its initial value $u0$
+# After defining all nodes, we can implement the spatial coordinate $x$ and its initial value $u0 = u(t_0)$
 # for every node.
 x = Matrix{Float64}(undef, length(nodes), n_elements)
 for element in 1:n_elements

docs/make.jl

@@ -28,19 +28,36 @@ DocMeta.setdocmeta!(Trixi2Vtk, :DocTestSetup, :(using Trixi2Vtk); recursive=true
 # as necessary
 # Based on: https://github.com/ranocha/SummationByPartsOperators.jl/blob/0206a74140d5c6eb9921ca5021cb7bf2da1a306d/docs/make.jl#L27-L41
 open(joinpath(@__DIR__, "src", "code_of_conduct.md"), "w") do io
-  # Point to source license file
-  println(io, """
-  ```@meta
-  EditURL = "https://github.com/trixi-framework/Trixi.jl/blob/main/CODE_OF_CONDUCT.md"
-  ```
-  """)
-  # Write the modified contents
-  println(io, "# [Code of Conduct](@id code-of-conduct)")
-  println(io, "")
-  for line in eachline(joinpath(dirname(@__DIR__), "CODE_OF_CONDUCT.md"))
-    line = replace(line, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref)")
-    println(io, "> ", line)
-  end
+    # Point to source license file
+    println(io,
+            """
+            ```@meta
+            EditURL = "https://github.com/trixi-framework/Trixi.jl/blob/main/CODE_OF_CONDUCT.md"
+            ```
+            """)
+    # Write the modified contents
+    println(io, "# [Code of Conduct](@id code-of-conduct)")
+    println(io, "")
+    for line in eachline(joinpath(dirname(@__DIR__), "CODE_OF_CONDUCT.md"))
+        line = replace(line, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref)")
+        println(io, "> ", line)
+    end
+end
+
+open(joinpath(@__DIR__, "src", "contributing.md"), "w") do io
+    # Point to source license file
+    println(io,
+            """
+            ```@meta
+            EditURL = "https://github.com/trixi-framework/Trixi.jl/blob/main/CONTRIBUTING.md"
+            ```
+            """)
+    # Write the modified contents
+    for line in eachline(joinpath(dirname(@__DIR__), "CONTRIBUTING.md"))
+      line = replace(line, "[LICENSE.md](LICENSE.md)" => "[License](@ref)")
+      line = replace(line, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref)")
+      println(io, line)
+    end
 end
 
 # Create tutorials for the following files:

examples/tree_1d_dgsem/elixir_euler_source_terms.jl

@@ -44,9 +44,12 @@ save_solution = SaveSolutionCallback(interval = 100,
 
 stepsize_callback = StepsizeCallback(cfl = 0.8)
 
+time_series = TimeSeriesCallback(semi, [0.0, 0.33, 1.0], interval = 10)
+
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         save_solution,
+                        time_series,
                         stepsize_callback)
 
 ###############################################################################

examples/tree_3d_dgsem/elixir_euler_source_terms.jl

@@ -41,9 +41,14 @@ save_solution = SaveSolutionCallback(interval = 100,
 
 stepsize_callback = StepsizeCallback(cfl = 0.6)
 
+time_series = TimeSeriesCallback(semi,
+                                 [(0.0, 0.0, 0.0), (0.33, 0.33, 0.33), (1.0, 1.0, 1.0)],
+                                 interval = 10)
+
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         save_solution,
+                        time_series,
                         stepsize_callback)
 
 ###############################################################################

examples/unstructured_2d_dgsem/elixir_euler_time_series.jl

@@ -0,0 +1,115 @@
+# An elixir that has an alternative convergence test that uses
+# the `TimeSeriesCallback` on several gauge points. Many of the
+# gauge points are selected as "stress tests" for the element
+# identification, e.g., a gauge point that lies on an
+# element corner of a curvilinear mesh
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the compressible Euler equations
+
+equations = CompressibleEulerEquations2D(1.4)
+
+# Modify the manufactured solution test to use `L = sqrt(2)`
+# in the initial condition and source terms
+function initial_condition_convergence_shifted(x, t,
+                                               equations::CompressibleEulerEquations2D)
+    c = 2
+    A = 0.1
+    L = sqrt(2)
+    f = 1 / L
+    ω = 2 * pi * f
+    ini = c + A * sin(ω * (x[1] + x[2] - t))
+
+    rho = ini
+    rho_v1 = ini
+    rho_v2 = ini
+    rho_e = ini^2
+
+    return SVector(rho, rho_v1, rho_v2, rho_e)
+end
+
+@inline function source_terms_convergence_shifted(u, x, t,
+                                                  equations::CompressibleEulerEquations2D)
+    # Same settings as in `initial_condition`
+    c = 2
+    A = 0.1
+    L = sqrt(2)
+    f = 1 / L
+    ω = 2 * pi * f
+    γ = equations.gamma
+
+    x1, x2 = x
+    si, co = sincos(ω * (x1 + x2 - t))
+    rho = c + A * si
+    rho_x = ω * A * co
+    # Note that d/dt rho = -d/dx rho = -d/dy rho.
+
+    tmp = (2 * rho - 1) * (γ - 1)
+
+    du1 = rho_x
+    du2 = rho_x * (1 + tmp)
+    du3 = du2
+    du4 = 2 * rho_x * (rho + tmp)
+
+    return SVector(du1, du2, du3, du4)
+end
+
+initial_condition = initial_condition_convergence_shifted
+
+source_term = source_terms_convergence_shifted
+
+###############################################################################
+# Get the DG approximation space
+
+solver = DGSEM(polydeg = 6, surface_flux = flux_lax_friedrichs)
+
+###############################################################################
+# Get the curved quad mesh from a file (downloads the file if not available locally)
+
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/b434e724e3972a9c4ee48d58c80cdcdb/raw/55c916cd8c0294a2d4a836e960dac7247b7c8ccf/mesh_multiple_flips.mesh",
+                           joinpath(@__DIR__, "mesh_multiple_flips.mesh"))
+
+mesh = UnstructuredMesh2D(mesh_file, periodicity = true)
+
+###############################################################################
+# create the semi discretization object
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
+                                    source_terms = source_term)
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+tspan = (0.0, 1.0)
+ode = semidiscretize(semi, tspan)
+
+summary_callback = SummaryCallback()
+
+analysis_interval = 1000
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
+
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
+
+time_series = TimeSeriesCallback(semi,
+                                 [(0.75, 0.7), (1.23, 0.302), (0.8, 1.0),
+                                     (0.353553390593274, 0.353553390593274),
+                                     (0.505, 1.125), (1.37, 0.89), (0.349, 0.7153),
+                                     (0.883883476483184, 0.406586401289607),
+                                     (sqrt(2), sqrt(2))];
+                                 interval = 10)
+
+callbacks = CallbackSet(summary_callback,
+                        analysis_callback,
+                        time_series,
+                        alive_callback)
+
+###############################################################################
+# run the simulation
+
+sol = solve(ode, RDPK3SpFSAL49(); abstol = 1.0e-6, reltol = 1.0e-6,
+            ode_default_options()..., callback = callbacks);
+
+summary_callback() # print the timer summary