Small modifications

.JuliaFormatter.toml

@@ -0,0 +1,8 @@
+# Use SciML style: https://github.com/SciML/SciMLStyle
+style = "sciml"
+
+# Python style alignment. See https://github.com/domluna/JuliaFormatter.jl/pull/732.
+yas_style_nesting = true
+
+# Align struct fields for better readability of large struct definitions
+align_struct_field = true

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/FormatCheck.yml

@@ -0,0 +1,44 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+
+jobs:
+  check-format:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
+        #
+        # TODO: Change the call below to
+        #       format(".")
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(["examples", "src", "test"])'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/[email protected]

.github/workflows/ci.yml

@@ -0,0 +1,63 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'LICENSE.md'
+      - 'README.md'
+  pull_request:
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'LICENSE.md'
+      - 'README.md'
+  workflow_dispatch:
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    # We could also include the Julia version as in
+    # name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - Julia ${{ matrix.version }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    # to be more specific. However, that requires us updating the required CI tests whenever we update Julia.
+    name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: ""
+      - name: Run tests with coverage
+        uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: true
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src,examples
+      - uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          flag-name: run-${{ matrix.trixi_test }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}-${{ github.run_id }}
+          parallel: false
+          path-to-lcov: ./lcov.info

.gitignore

@@ -0,0 +1,33 @@
+*.pdf
+*.png
+*.h5
+*.mp4
+*.mem
+*.vtu
+*.pvd
+*.avi
+*.ogv
+*.mesh
+*.bson
+*.inp
+**/Manifest.toml
+out*/
+docs/build
+docs/src/notebooks
+docs/src/authors.md
+docs/src/tutorials
+public/
+coverage/
+coverage_report/
+**/*.jl.*.cov
+**/.ipynb_checkpoints/
+**/solution_*.txt
+**/restart_*.txt
+.vscode/
+
+.DS_Store
+
+run
+run/*
+
+LocalPreferences.toml

.typos.toml

@@ -0,0 +1,4 @@
+[default.extend-words]
+rcall = "rcall"
+claus = "claus"
+dum = "dum"

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023-present Michael Schlottke-Lakemper, Julia Odenthal
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

@@ -0,0 +1,15 @@
+name = "TrixiSmartShockFinder"
+uuid = "6b42f25e-8cc0-41c2-936f-439385811e39"
+authors = ["Michael Schlottke-Lakemper <[email protected]> and contributors"]
+version = "0.1.0"
+
+[deps]
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
+Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
+
+[compat]
+Flux = "0.13.15, 0.14"
+MuladdMacro = "0.2.4"
+# Trixi = "0.6"
+julia = "1.9"

README.md

@@ -1,2 +1,47 @@
 # TrixiSmartShockFinder.jl
-Spin-off repository of Trixi.jl with neural network-based shock indicators
+[![Build Status](https://github.com/trixi-framework/TrixiSmartShockFinder.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/TrixiSmartShockFinder.jl/actions?query=workflow%3ACI)
+[![Coveralls](https://coveralls.io/repos/github/trixi-framework/TrixiSmartShockFinder.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/TrixiSmartShockFinder.jl?branch=main)
+[![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
+
+Spin-off repository of [Trixi.jl](https://github.com/trixi-framework/Trixi.jl)
+with neural network-based shock indicators.
+
+**Note: This repository is currently not under development and has been archived. If you are
+interested in using any of this, please get in touch with the developers of the
+[Trixi.jl](https://github.com/trixi-framework/Trixi.jl) package.
+
+
+## Usage
+To run any of the elixirs with the neurl network-based indicators, you first need to install
+all required auxiliary packages by running the following code in the Julia REPL:
+```julia
+julia> using Pkg
+
+julia> Pkg.add(["BSON", "Flux", "OrdinaryDiffEq", "Trixi"])
+```
+
+Then, clone this repository
+```shell
+git clone [email protected]:trixi-framework/TrixiSmartShockFinder.jl.git
+```
+enter the directory, and start Julia (tested with Julia v1.9) with the project set to
+the clone directory
+```
+cd TrixiSmartShockFinder.jl
+julia --project=.
+```
+
+Now run one of the elixirs in the `examples` folder, e.g.,
+```julia
+using TrixiSmartShockFinder
+trixi_include("examples/tree_2d_dgsem/elixir_euler_blast_wave_neuralnetwork_perssonperaire.jl")
+```
+
+## Authors
+TrixiSmartShockFinder.jl was initiated by
+[Michael Schlottke-Lakemper](https://lakemper.eu) (University of Augsburg, Germany) and
+Julia Odenthal (University of Cologne, Germany).
+
+
+## License and contributing
+TrixiSmartShockFinder.jl is licensed under the MIT license (see [LICENSE.md](LICENSE.md)).

examples/tree_1d_dgsem/elixir_euler_blast_wave_neuralnetwork_perssonperaire.jl

@@ -0,0 +1,115 @@
+using Downloads: download
+using Flux
+using BSON: load
+network = joinpath(@__DIR__, "modelnnpp-0.97-0.0001.bson")
+download("https://github.com/trixi-framework/Trixi_IndicatorNeuralNetwork_networks/raw/main/networks/modelnnpp-0.97-0.0001.bson",
+         network)
+model1d = load(network, @__MODULE__)[:model1d]
+
+using OrdinaryDiffEq
+using TrixiSmartShockFinder
+using Trixi
+
+# TODO: Remove once Trixi.jl is released without these exports
+NeuralNetworkPerssonPeraire = TrixiSmartShockFinder.NeuralNetworkPerssonPeraire
+NeuralNetworkRayHesthaven = TrixiSmartShockFinder.NeuralNetworkRayHesthaven
+IndicatorNeuralNetwork = TrixiSmartShockFinder.IndicatorNeuralNetwork
+
+# This elixir was one of the setups used in the following master thesis:
+# - Julia Odenthal (2021)
+#   Shock capturing with artificial neural networks
+#   University of Cologne, advisors: Gregor Gassner, Michael Schlottke-Lakemper
+# This motivates the particular choice of fluxes, mesh resolution etc.
+
+###############################################################################
+# semidiscretization of the compressible Euler equations
+
+equations = CompressibleEulerEquations1D(1.4)
+
+"""
+    initial_condition_blast_wave(x, t, equations::CompressibleEulerEquations1D)
+
+A medium blast wave taken from
+- Sebastian Hennemann, Gregor J. Gassner (2020)
+  A provably entropy stable subcell shock capturing approach for high order split form DG
+  [arXiv: 2008.12044](https://arxiv.org/abs/2008.12044)
+"""
+function initial_condition_blast_wave(x, t, equations::CompressibleEulerEquations1D)
+    # Modified From Hennemann & Gassner JCP paper 2020 (Sec. 6.3) -> "medium blast wave"
+    # Set up polar coordinates
+    inicenter = SVector(0.0)
+    x_norm = x[1] - inicenter[1]
+    r = abs(x_norm)
+    # The following code is equivalent to
+    # phi = atan(0.0, x_norm)
+    # cos_phi = cos(phi)
+    # in 1D but faster
+    cos_phi = x_norm > 0 ? one(x_norm) : -one(x_norm)
+
+    # Calculate primitive variables
+    rho = r > 0.5 ? 1.0 : 1.1691
+    v1 = r > 0.5 ? 0.0 : 0.1882 * cos_phi
+    p = r > 0.5 ? 1.0E-3 : 1.245
+
+    return prim2cons(SVector(rho, v1, p), equations)
+end
+initial_condition = initial_condition_blast_wave
+
+surface_flux = flux_lax_friedrichs
+volume_flux = flux_chandrashekar
+basis = LobattoLegendreBasis(3)
+indicator_sc = IndicatorNeuralNetwork(equations, basis,
+                                      indicator_type = NeuralNetworkPerssonPeraire(),
+                                      alpha_max = 0.5,
+                                      alpha_min = 0.001,
+                                      alpha_smooth = true,
+                                      alpha_continuous = false,
+                                      alpha_amr = false,
+                                      variable = density_pressure,
+                                      network = model1d)
+volume_integral = VolumeIntegralShockCapturingHG(indicator_sc;
+                                                 volume_flux_dg = volume_flux,
+                                                 volume_flux_fv = surface_flux)
+solver = DGSEM(basis, surface_flux, volume_integral)
+
+coordinates_min = (-2.0,)
+coordinates_max = (2.0,)
+mesh = TreeMesh(coordinates_min, coordinates_max,
+                initial_refinement_level = 6,
+                n_cells_max = 10_000)
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+tspan = (0.0, 12.5)
+ode = semidiscretize(semi, tspan)
+
+summary_callback = SummaryCallback()
+
+analysis_interval = 100
+
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
+
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
+
+save_solution = SaveSolutionCallback(interval = 100,
+                                     save_initial_solution = true,
+                                     save_final_solution = true,
+                                     solution_variables = cons2prim)
+
+stepsize_callback = StepsizeCallback(cfl = 0.5)
+
+callbacks = CallbackSet(summary_callback,
+                        analysis_callback, alive_callback,
+                        save_solution,
+                        stepsize_callback)
+
+###############################################################################
+# run the simulation
+
+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);
+summary_callback() # print the timer summary