Merge branch 'main' into subcell-limiting-entropies

trixi-framework · Mar 25, 2024 · 08e9f97 · 08e9f97
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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
@@ -7,8 +7,9 @@ for human readability.
 ## Changes in the v0.7 lifecycle
 
 #### Added
-- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D`.
-- Subcell local one-sided limiting support for nonlinear variables in 2D for `TreeMesh`
+- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension
+  to 1D and 3D on `TreeMesh`.
+- Subcell local one-sided limiting support for nonlinear variables in 2D for `TreeMesh`.
 
 
 ## 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 = "0.7.5-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"

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/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_3d_dgsem/elixir_euler_source_terms.jl b/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)
 
 ###############################################################################

diff --git a/src/Trixi.jl b/src/Trixi.jl
@@ -22,7 +22,7 @@ using LinearAlgebra: LinearAlgebra, Diagonal, diag, dot, mul!, norm, cross, norm
                      UniformScaling, det
 using Printf: @printf, @sprintf, println
 using SparseArrays: AbstractSparseMatrix, AbstractSparseMatrixCSC, sparse, droptol!,
-                    rowvals, nzrange, nonzeros, spzeros
+                    rowvals, nzrange, nonzeros
 
 # import @reexport now to make it available for further imports/exports
 using Reexport: @reexport
@@ -32,10 +32,10 @@ using Reexport: @reexport
 using MPI: MPI
 
 using SciMLBase: CallbackSet, DiscreteCallback,
-                 ODEProblem, ODESolution, ODEFunction,
+                 ODEProblem, ODESolution,
                  SplitODEProblem
 import SciMLBase: get_du, get_tmp_cache, u_modified!,
-                  AbstractODEIntegrator, init, step!, check_error,
+                  init, step!, check_error,
                   get_proposed_dt, set_proposed_dt!,
                   terminate!, remake, add_tstop!, has_tstop, first_tstop
 
@@ -57,7 +57,6 @@ using Polyester: Polyester, @batch # You know, the cheapest threads you can find
 using OffsetArrays: OffsetArray, OffsetVector
 using P4est
 using T8code
-using Setfield: @set
 using RecipesBase: RecipesBase
 using Requires: @require
 using Static: Static, One, True, False
@@ -66,7 +65,7 @@ using StaticArrays: StaticArrays, MVector, MArray, SMatrix, @SMatrix
 using StrideArrays: PtrArray, StrideArray, StaticInt
 @reexport using StructArrays: StructArrays, StructArray
 using TimerOutputs: TimerOutputs, @notimeit, TimerOutput, print_timer, reset_timer!
-using Triangulate: Triangulate, TriangulateIO, triangulate
+using Triangulate: Triangulate, TriangulateIO
 export TriangulateIO # for type parameter in DGMultiMesh
 using TriplotBase: TriplotBase
 using TriplotRecipes: DGTriPseudocolor
@@ -84,9 +83,9 @@ const _PREFERENCE_LOG = @load_preference("log", "log_Trixi_NaN")
 
 # finite difference SBP operators
 using SummationByPartsOperators: AbstractDerivativeOperator,
-                                 AbstractNonperiodicDerivativeOperator, DerivativeOperator,
+                                 AbstractNonperiodicDerivativeOperator,
                                  AbstractPeriodicDerivativeOperator,
-                                 PeriodicDerivativeOperator, grid
+                                 grid
 import SummationByPartsOperators: integrate, semidiscretize,
                                   compute_coefficients, compute_coefficients!,
                                   left_boundary_weight, right_boundary_weight

diff --git a/src/auxiliary/auxiliary.jl b/src/auxiliary/auxiliary.jl
@@ -242,6 +242,8 @@ macro threaded(expr)
     # !!! danger "Heisenbug"
     #     Look at the comments for `wrap_array` when considering to change this macro.
 
+    # By using `Trixi.@batch` we allow users of Trixi.jl to use `@threaded` without having
+    # Polyester.jl in their namespace.
     return esc(quote
                    Trixi.@batch $(expr)
                end)

diff --git a/src/callbacks_step/time_series.jl b/src/callbacks_step/time_series.jl
@@ -23,8 +23,7 @@ After the last time step, the results are stored in an HDF5 file `filename` in d
 The real data type `RealT` and data type for solution variables `uEltype` default to the respective
 types used in the solver and the cache.
 
-Currently this callback is only implemented for [`TreeMesh`](@ref) in 2D
-and [`UnstructuredMesh2D`](@ref).
+Currently this callback is only implemented for [`TreeMesh`](@ref) and [`UnstructuredMesh2D`](@ref).
 """
 mutable struct TimeSeriesCallback{RealT <: Real, uEltype <: Real, SolutionVariables,
                                   VariableNames, Cache}
@@ -218,5 +217,6 @@ function (time_series_callback::TimeSeriesCallback)(integrator)
 end
 
 include("time_series_dg.jl")
-include("time_series_dg2d.jl")
+include("time_series_dg_tree.jl")
+include("time_series_dg_unstructured.jl")
 end # @muladd
diff --git a/src/callbacks_step/time_series_dg.jl b/src/callbacks_step/time_series_dg.jl
@@ -34,4 +34,41 @@ function save_time_series_file(time_series_callback,
         end
     end
 end
+
+# Creates cache for time series callback
+function create_cache_time_series(point_coordinates,
+                                  mesh::Union{TreeMesh, UnstructuredMesh2D},
+                                  dg, cache)
+    # Determine element ids for point coordinates
+    element_ids = get_elements_by_coordinates(point_coordinates, mesh, dg, cache)
+
+    # Calculate & store Lagrange interpolation polynomials
+    interpolating_polynomials = calc_interpolating_polynomials(point_coordinates,
+                                                               element_ids, mesh,
+                                                               dg, cache)
+
+    time_series_cache = (; element_ids, interpolating_polynomials)
+
+    return time_series_cache
+end
+
+function get_elements_by_coordinates(coordinates, mesh, dg, cache)
+    element_ids = Vector{Int}(undef, size(coordinates, 2))
+    get_elements_by_coordinates!(element_ids, coordinates, mesh, dg, cache)
+
+    return element_ids
+end
+
+function calc_interpolating_polynomials(coordinates, element_ids,
+                                        mesh::Union{TreeMesh, UnstructuredMesh2D},
+                                        dg, cache)
+    interpolating_polynomials = Array{real(dg), 3}(undef,
+                                                   nnodes(dg), ndims(mesh),
+                                                   length(element_ids))
+    calc_interpolating_polynomials!(interpolating_polynomials, coordinates, element_ids,
+                                    mesh, dg,
+                                    cache)
+
+    return interpolating_polynomials
+end
 end # @muladd