carlodev · carlodev · Nov 30, 2023 · Nov 30, 2023 · Nov 30, 2023 · Nov 30, 2023
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -3,42 +3,115 @@ on:
   push:
     branches:
       - master
-      - SEM-coupling
     tags: ['*']
+
 jobs:
-  VMSTests:
-    name: VMS Tests
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1.8.2'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
+  REPLTestsCommons:
+    name: Sequential-Commons
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@latest
         with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
+          version: '1.11.1'
+          arch: x64
+      - uses: actions/cache@v4
         with:
           path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+          key: ubuntu-test-cache-${{ hashFiles('**/Project.toml') }}
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - uses: actions/upload-artifact@v4
         with:
-          threshold:  70%
+          name: coverage-sequential-commons
+          path: ./lcov.info
+
+  REPLTestsCases:
+    name: Sequential-Cases
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.11.1'
+          arch: x64
+      - uses: actions/cache@v4
+        with:
+          path: ~/.julia/artifacts
+          key: ubuntu-test-cache-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - run: julia --code-coverage --project=. -e "include(joinpath(\"test\", \"sequential\", \"runcases.jl\"))"
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: actions/upload-artifact@v4
+        with:
+          name: coverage-sequential-cases
+          path: ./lcov.info
+
+  UtilsTests:
+    name: Sequential-Utils
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.11.1'
+          arch: x64
+      - uses: actions/cache@v4
+        with:
+          path: ~/.julia/artifacts
+          key: ubuntu-test-cache-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - run: julia --code-coverage --project=. -e "include(joinpath(\"test\", \"UtilsTests\", \"runtests.jl\"))"
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: actions/upload-artifact@v4
+        with:
+          name: coverage-sequential-utils
+          path: ./lcov.info
+
+  MPITests:
+    name: SegregatedVMSSolver-MPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.11.1'
+          arch: x64
+      - uses: actions/cache@v4
+        with:
+          path: ~/.julia/artifacts
+          key: ubuntu-mpi-test-cache-${{ hashFiles('**/Project.toml') }}
+      - uses: julia-actions/julia-buildpkg@v1
+      - run: julia --project=. -e "include(joinpath(\"test\", \"mpi\", \"runtests.jl\"))"
+
+  mergeCoverage:
+    name: Merge Coverage & Upload
+    runs-on: ubuntu-latest
+    needs: [REPLTestsCommons, REPLTestsCases, UtilsTests]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v4
+        with:
+          path: coverage_reports
+      - run: julia --project=. -e '
+          using Pkg;
+          Pkg.activate(temp=true);
+          Pkg.add("Coverage");
+          using Coverage;
+          coverage = LCOV.readfolder(".");
+          for cov in coverage
+            cov.filename = replace(cov.filename, "\\" => "/")
+          end;
+          coverage = merge_coverage_counts(coverage);
+          @show covered_lines, total_lines = get_summary(coverage)
+          LCOV.writefile("./lcov.info", coverage);'
+      - uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./lcov.info
+      - uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: codecov-lcov
+          files: lcov.info
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.8.2'
+          version: '1.11.1'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "SegregatedVMSSolver"
 uuid = "90220dfc-fac3-4908-b895-51c1a1f4cb85"
 authors = ["Carlo Brunelli"]
-version = "2.0.1"
+version = "3.0.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -20,35 +20,39 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 ScatteredInterpolation = "3f865c0f-6dca-5f4d-999b-29fe1e7e3c92"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SyntheticEddyMethod = "57cf2c78-4fcb-4d27-9f1f-369b8b08b789"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Trapz = "592b5752-818d-11e9-1e9a-2b8ca4a44cd1"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-CSV = "0.10.11"
-DataFrames = "1.6.1"
+CSV = "0.10.15"
+DataFrames = "1.7.0"
+DataInterpolations = "6.6.0"
+DelimitedFiles = "1.9.1"
 FFTW = "1.8.0"
-FillArrays = "1.7.0"
-Gridap = "0.17.20"
-GridapDistributed = "0.3.2"
-GridapGmsh = "0.7.1"
-GridapPETSc = "0.5.0"
-MPI = "0.20.16"
-NearestNeighbors = "0.4.16"
+FileIO = "1.16.6"
+FillArrays ="=1.13.0"
+Gridap = "=0.17.20"
+GridapDistributed = "=0.3.2"
+GridapGmsh = "=0.7.1"
+GridapPETSc = "=0.5.3"
+MPI ="=0.20.22"
+NearestNeighbors ="0.4.21"
 Parameters = "0.12.3"
-PartitionedArrays = "0.3.4"
-Revise = "3.5.9"
+PartitionedArrays ="=0.3.4"
+Revise ="3.7.1"
 ScatteredInterpolation = "0.3.6"
-Trapz = "2.0.3"
-julia = "1.8.2"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]
+LinearAlgebra = "1.11.0"
+SparseArrays = "1.11.0"
+SyntheticEddyMethod = "=0.4.4"
+Trapz ="2.0.3"
+Test = "1.11.0"
+UnPack = "1.0.2"
+julia = "1.11.1"
diff --git a/README.md b/README.md
@@ -12,11 +12,11 @@
 ![Julia flow](docs/figs/DU89.gif)
 
 ## Introduction
-The package solves the incompressible Navier-Stokes equations using SUPG and VMS method. VMS has been originally introduced by [Hughes2000](@cite). In specific, a linearized and segregated version of the SUPG (following the steps illustrated by [Janssens2014](@cite)) and VMS is solved. 
+The package solves the incompressible Navier-Stokes equations in the Finite Element Framework using SUPG and VMS method. VMS has been originally introduced by [Hughes2000](@cite). In specific, a linearized and segregated version of the SUPG (following the steps illustrated by [Janssens2014](@cite)) and VMS is solved. 
 
-The methods belong to the Large Eddy Simulation (LES) family. The package can solve the `Taylor Green Vortices` (only 2D), `Lid Driven Cavity Flow` (only 2D), `Cylinder vortex shedding` (only 2D), and general `Airfoils` (2D and 3D). 
+The methods belong to the Large Eddy Simulation (LES) family. The package can solve the `Taylor Green Vortices`, `Lid Driven Cavity Flow` (only 2D), `Cylinder vortex shedding` and and general `Airfoils` (2D and 3D). 
 
-It works fully in parallel (tested up to 80-CORES). It is specialized for the resolution of flow over airfoils, testing the capability of detecting the Laminar Separation Bubble. It is equipped with some utility `modules` for reading the output files and creating proper initial conditions.
+It works fully in parallel. It is specialized for the resolution of flow over airfoils, testing the capability of detecting the Laminar Separation Bubble. It is equipped with some utility `modules` for reading the output files and creating proper initial conditions.
 
 ## Installation
 The package is registered, so you can install it as:
@@ -50,5 +50,37 @@ For creating mesh and physical boundary conditions is suggested to install the f
 - Possibility of choosing the backend thanks to `PartitionedArrays.jl`. It can be run in the `REPL` for debugging or in `MPI`
 
 
+## Examples
+
+| ![](docs/figs/TGV.gif)  [Taylor-Green Vortices](https://carlodev.github.io/SegregatedVMSSolver.jl/dev/Cases/taylorgreen/) |  ![](docs/figs/Ldx.png)  [Lid Driven Cavity Flow](https://carlodev.github.io/SegregatedVMSSolver.jl/dev/Cases/liddriven/) |
+|:-------------:|:-------------:|
+
+| ![](docs/figs/Cyl3D.gif)  [Cylinder Vortex Shedding](https://carlodev.github.io/SegregatedVMSSolver.jl/dev/Cases/cylinder/)  | ![](docs/figs/DU89.gif) [Airfoil](https://carlodev.github.io/SegregatedVMSSolver.jl/dev/Cases/airfoil/)   | 
+|:-------------:|:-------------:|
+
+
+## Parallelization
+For parallelization is used `MPI`, and to solve the sparse and distribute numerical systems we use `PETSc`.
+The benchmark case is the 2D taylor Green, the time reported here are intended for each time-step. The order of the elements for this simulation is always 2, and the CFL constant at 0.32.
+
+### Strong Parallelization
+Strong scalability evaluates how efficiently a parallel code reduces execution time when the problem size remains fixed, but the number of processing units increases. There is a total of `400` elements on each side, leading to `160000` elements and `1920000` dofs in total.
+![MPI-strong](docs/figs/STRONG_TGV.png)
+
+
+### Weak Parallelization
+Weak scalability measures how well a parallel code maintains performance when the problem size is kept constant per processor, and the number of processors increases. On each processor there are `50x50` elements, the number of dofs is kept constant at `30K dfos/procs`.
+![MPI-weak](docs/figs/WEAK_TGV.png)
+
+
+
 ## Packages
-It relies on the  [`Gridap`](https://github.com/gridap/Gridap.jl) ecosystem. It is also completely written in Julia and allows parallelization. The [`MPI`](https://github.com/JuliaParallel/MPI.jl) and [`PartititionedArrays`](https://github.com/fverdugo/PartitionedArrays.jl) are also at the basis of the parallelization.
+It relies on the  [`Gridap`](https://github.com/gridap/Gridap.jl) ecosystem. It is also completely written in Julia and allows parallelization. The [`MPI`](https://github.com/JuliaParallel/MPI.jl) and [`PartititionedArrays`](https://github.com/fverdugo/PartitionedArrays.jl) are also at the basis of the parallelization.
+
+
+
+## Contributing
+It is a collaborative project open to contributions. You can:
+- Open a new issue
+- Contact the project administator
+- Open a PR with the contribution
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -5,5 +5,5 @@ DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 SegregatedVMSSolver = "90220dfc-fac3-4908-b895-51c1a1f4cb85"
 
 [compat]
-Documenter = "0.27.23"
-DocumenterCitations = "1.0.0"
+Documenter = "1.8.0"
+DocumenterCitations = "1.3.5"
diff --git a/docs/figs/Cyl3D.gif b/docs/figs/Cyl3D.gif
diff --git a/docs/figs/DU89-LSB.gif b/docs/figs/DU89-LSB.gif
diff --git a/docs/figs/LS-VMS-LD-1000.png b/docs/figs/LS-VMS-LD-1000.png
diff --git a/docs/figs/Ldx.png b/docs/figs/Ldx.png
diff --git a/docs/figs/STRONG_TGV.png b/docs/figs/STRONG_TGV.png
diff --git a/docs/figs/TGV.gif b/docs/figs/TGV.gif
diff --git a/docs/figs/WEAK_TGV.png b/docs/figs/WEAK_TGV.png
diff --git a/docs/make.jl b/docs/make.jl
@@ -6,25 +6,34 @@ using Documenter, DocumenterCitations, SegregatedVMSSolver
 bib = CitationBibliography(joinpath(@__DIR__, "src", "docs.bib"); style=:numeric)
 
 
-makedocs(bib;
+makedocs(;plugins=[bib],
     sitename = "SegregatedVMSSolver.jl",
     modules = [SegregatedVMSSolver],
     pages = [
         "Introduction" => "index.md",
-        "User Parameters" => "user_params.md",
-        "Simulation Parameters" => "sim_params.md",
+        "Parameters Guide" => [
+        "User Parameters"=>"user_params.md",
+        "Simulation Parameters" => "sim_params.md"],
+
         "MPI run" => "mpi.md",
-        "Cases" =>[
-        "Airfoil" => "Cases/airfoil.md",
-        "Taylor Green" => "Cases/taylorgreen.md",
-        "Lid Driven Cavity Flow" => "Cases/liddriven.md",
+        "Examples" =>[
+        "Intro"=>"Cases/examples.md",
+        "Taylor Green 2D" => "Cases/taylorgreen2D.md",
+        "Taylor Green 3D" => "Cases/taylorgreen3D.md",
+        "Lid Driven Cavity Flow" => "Cases/liddriven.md",        
         "Cylinder" => "Cases/cylinder.md",
+        "Airfoil" => "Cases/airfoil.md",
+        "Create your Own Case" => "create_case.md",
         ],
-        "Restart" => "restart.md",
-
-        "Post Processing" => "post_proc.md",
-        "Boundary Layer Initialization" => "blinit.md",
-
+        "Theory"=>[
+            "Incompressible Navier Stokes"=>"Theory/NS_inc.md",
+            "FEM"=>"Theory/FEMTheory.md",
+            "SUPG & VMS Stabilization"=>"Theory/SUPG_VMS_stab.md",
+            "Error and Parallelization"=>"Theory/Errors.md"],
+        "Tools"=>[       
+        "Visualization" => "Tools/visualization.md",
+        "Post Processing" => "Tools/post_proc.md",
+        "Boundary Layer Initialization" => "Tools/blinit.md"],
         "API information" => "api_info.md",
         "References" => "references.md",
     ],