Merge branch 'main' into surface_pressure_forces

trixi-framework · Mar 27, 2024 · 8aaab77 · 8aaab77
2 parents d0a1e3e + 73da92c
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diff --git a/CONTRIBUTING.md b/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

diff --git a/NEWS.md b/NEWS.md
@@ -8,6 +8,8 @@ for human readability.
 
 #### Added
 - Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D`.
+- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension
+  to 1D and 3D on `TreeMesh`.
 - Pressure lift and drag coefficients can now be computed for 2D `P4estMesh`.
 
 ## Changes when updating to v0.7 from v0.6.x

diff --git a/Project.toml b/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 = "0.7.4-pre"
+version = "0.7.6-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"
@@ -76,15 +75,14 @@ MuladdMacro = "0.2.2"
 Octavian = "0.3.21"
 OffsetArrays = "1.12"
 P4est = "0.4.9"
-Polyester = "0.7.5"
+Polyester = "0.7.10"
 PrecompileTools = "1.1"
 Preferences = "1.3"
 Printf = "1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
 SciMLBase = "1.90, 2"
-Setfield = "1"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
 StartUpDG = "0.17.7"

diff --git a/README.md b/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) -->
 

diff --git a/SECURITY.md b/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.
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -1 +1,3 @@
 src/code_of_conduct.md
+src/contributing.md
+
diff --git a/docs/make.jl b/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:

diff --git a/docs/src/contributing.md b/docs/src/contributing.md
diff --git a/docs/src/performance.md b/docs/src/performance.md
@@ -282,14 +282,3 @@ requires. It can thus be seen as a proxy for "energy used" and, as an extension,
     timing result, you need to set the analysis interval such that the
     `AnalysisCallback` is invoked at least once during the course of the simulation and
     discard the first PID value.
-
-## Performance issues with multi-threaded reductions
-[False sharing](https://en.wikipedia.org/wiki/False_sharing) is a known performance issue
-for systems with distributed caches. It also occurred for the implementation of a thread
-parallel bounds checking routine for the subcell IDP limiting
-in [PR #1736](https://github.com/trixi-framework/Trixi.jl/pull/1736).
-After some [testing and discussion](https://github.com/trixi-framework/Trixi.jl/pull/1736#discussion_r1423881895),
-it turned out that initializing a vector of length `n * Threads.nthreads()` and only using every
-n-th entry instead of a vector of length `Threads.nthreads()` fixes the problem.
-Since there are no processors with caches over 128B, we use `n = 128B / size(uEltype)`.
-Now, the bounds checking routine of the IDP limiting scales as hoped.
diff --git a/examples/dgmulti_2d/elixir_navierstokes_lid_driven_cavity.jl b/examples/dgmulti_2d/elixir_navierstokes_lid_driven_cavity.jl
@@ -4,12 +4,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the ideal compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 0.001
+mu = 0.001
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 # Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux

diff --git a/examples/dgmulti_3d/elixir_navierstokes_taylor_green_vortex.jl b/examples/dgmulti_3d/elixir_navierstokes_taylor_green_vortex.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 6.25e-4 # equivalent to Re = 1600
+mu = 6.25e-4 # equivalent to Re = 1600
 
 equations = CompressibleEulerEquations3D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 """

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl b/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl
@@ -4,12 +4,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the ideal compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 0.001
+mu = 0.001
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 # Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity_amr.jl b/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity_amr.jl
@@ -4,12 +4,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the ideal compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 0.001
+mu = 0.001
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 # Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux

diff --git a/examples/p4est_3d_dgsem/elixir_navierstokes_blast_wave_amr.jl b/examples/p4est_3d_dgsem/elixir_navierstokes_blast_wave_amr.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 6.25e-4 # equivalent to Re = 1600
+mu = 6.25e-4 # equivalent to Re = 1600
 
 equations = CompressibleEulerEquations3D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 function initial_condition_3d_blast_wave(x, t, equations::CompressibleEulerEquations3D)

diff --git a/examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex.jl b/examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 6.25e-4 # equivalent to Re = 1600
+mu = 6.25e-4 # equivalent to Re = 1600
 
 equations = CompressibleEulerEquations3D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 """

diff --git a/examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl b/examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 6.25e-4 # equivalent to Re = 1600
+mu = 6.25e-4 # equivalent to Re = 1600
 
 equations = CompressibleEulerEquations3D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion3D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 """

diff --git a/examples/tree_1d_dgsem/elixir_euler_source_terms.jl b/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)
 
 ###############################################################################

diff --git a/examples/tree_1d_dgsem/elixir_navierstokes_convergence_periodic.jl b/examples/tree_1d_dgsem/elixir_navierstokes_convergence_periodic.jl
@@ -5,7 +5,6 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
 mu() = 6.25e-4 # equivalent to Re = 1600
 

diff --git a/examples/tree_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl b/examples/tree_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl
@@ -4,12 +4,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the ideal compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 0.001
+mu = 0.001
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 # Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux

diff --git a/examples/tree_2d_dgsem/elixir_navierstokes_shearlayer_amr.jl b/examples/tree_2d_dgsem/elixir_navierstokes_shearlayer_amr.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 1.0 / 3.0 * 10^(-5) # equivalent to Re = 30,000
+mu = 1.0 / 3.0 * 10^(-4) # equivalent to Re = 30,000
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 """

diff --git a/examples/tree_2d_dgsem/elixir_navierstokes_taylor_green_vortex.jl b/examples/tree_2d_dgsem/elixir_navierstokes_taylor_green_vortex.jl
@@ -5,12 +5,11 @@ using Trixi
 ###############################################################################
 # semidiscretization of the compressible Navier-Stokes equations
 
-# TODO: parabolic; unify names of these accessor functions
 prandtl_number() = 0.72
-mu() = 6.25e-4 # equivalent to Re = 1600
+mu = 6.25e-4 # equivalent to Re = 1600
 
 equations = CompressibleEulerEquations2D(1.4)
-equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu(),
+equations_parabolic = CompressibleNavierStokesDiffusion2D(equations, mu = mu,
                                                           Prandtl = prandtl_number())
 
 """