Merge pull request #40 from zjwegert/src_refactor_and_docs

Documenter and refactor

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -0,0 +1,55 @@
+name: CI
+on: [push, pull_request]
+jobs:
+  test:
+    name: Tests ${{ matrix.version }} - ${{ 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@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        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 }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+
+#  docs:
+#    name: Documentation
+#    runs-on: ubuntu-latest
+#    steps:
+#      - uses: actions/checkout@v2
+#      - uses: julia-actions/setup-julia@v1
+#        with:
+#          version: '1.9'
+#      - run: |
+#          julia --project=docs -e '
+#            using Pkg
+#            Pkg.develop(PackageSpec(path=pwd()))
+#            Pkg.instantiate()'
+#      - run: julia --project=docs docs/make.jl
+#        env:
+#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci_mpi.yml

@@ -0,0 +1,70 @@
+name: CI_MPI
+on: [push, pull_request]
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    env:
+      P4EST_ROOT_DIR: "/opt/p4est/2.2/"
+      JULIA_PETSC_LIBRARY: "/opt/petsc/3.18/lib/libpetsc"
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache p4est
+        id: cache-p4est
+        uses: actions/cache@v2
+        with:
+         path: ${{env.P4EST_ROOT_DIR}}
+         key: ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
+         restore-keys: |
+           ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
+           ${{ runner.os }}-build-
+           ${{ runner.os }}-
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - name: Install p4est/petsc dependencies
+        run: |
+          sudo apt-get update 
+          sudo apt-get install -y wget gfortran g++ openmpi-bin libopenmpi-dev 
+      - name: Install petsc
+        run: |
+          CURR_DIR=$(pwd)
+          PACKAGE=petsc
+          VERSION=3.18
+          INSTALL_ROOT=/opt
+          PETSC_INSTALL=$INSTALL_ROOT/$PACKAGE/$VERSION
+          TAR_FILE=$PACKAGE-$VERSION.tar.gz
+          URL="https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
+          ROOT_DIR=/tmp
+          SOURCES_DIR=$ROOT_DIR/$PACKAGE-$VERSION
+          BUILD_DIR=$SOURCES_DIR/build
+          wget -q $URL/$TAR_FILE -O $ROOT_DIR/$TAR_FILE
+          mkdir -p $SOURCES_DIR
+          tar xzf $ROOT_DIR/$TAR_FILE -C $SOURCES_DIR --strip-components=1
+          cd $SOURCES_DIR
+          ./configure --prefix=$PETSC_INSTALL --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 \
+             --download-mumps --download-scalapack --download-parmetis --download-metis \
+             --download-ptscotch --with-debugging --with-x=0 --with-shared=1 \
+             --with-mpi=1 --with-64-bit-indices
+          make
+          make install
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: echo $PWD
+      - run: julia --project=. -e 'using Pkg; Pkg.instantiate();'
+      - run: julia --project=. -e 'using Pkg; Pkg.add("MPIPreferences")'
+      - run: julia --project=. -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
+      - run: julia --project=. -e 'using Pkg; Pkg.build(); Pkg.precompile()'
+      - run: julia --project=. --color=yes --check-bounds=yes test/mpi/runtests.jl
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.gitignore

@@ -28,4 +28,4 @@ results/*
 # environment.
 Manifest.toml
 LocalPreferences.toml
-LSTO_Distributed.so
+LevelSetTopOpt.so

Deprecated/Deprecated_root_files/Utilities.jl

@@ -30,7 +30,7 @@ Base.@kwdef struct SmoothErsatzMaterialInterpolation{M<:AbstractFloat}
 end
 
 write_vtk(Ω,path,φh,uh,H) = writevtk(Ω,path,cellfields=["phi"=>φh,
-    "H(phi)"=>(H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh)),"uh"=>uh])
+    "H(phi)"=>(H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh)),"uh"=>uh])
 
 # Update layout of ghost nodes to match columns of stiffness matrix
 function correct_ghost_layout(xh::DistributedCellField,cols)

Deprecated/Deprecated_root_files/auto_diff_elastic_compliance_parallel.jl

@@ -99,7 +99,7 @@ function main(mesh_partition,distribute)
     # path = dirname(dirname(@__DIR__))*"/results/AutoDiffTesting_Parallel";
     # writevtk(Ω,path,cellfields=["phi"=>φh,
     #     "H(phi)"=>(interp.H ∘ φh),
-    #     "|nabla(phi))|"=>(norm ∘ ∇(φh)),
+    #     "|nabla(phi)|"=>(norm ∘ ∇(φh)),
     #     "uh"=>uh,
     #     "J′_analytic"=>FEFunction(U_reg,dF_analytic),
     #     "J′_autodiff"=>FEFunction(U_reg,dF),

Deprecated/Deprecated_root_files/inverse_homogenisation_parallel.jl

@@ -113,7 +113,7 @@ function main(mesh_partition,distribute)
     path = dirname(dirname(@__DIR__))*"/results/InvHomLE_AutoDiffTesting_Parallel";
     writevtk(Ω,path,cellfields=["phi"=>φh,
         "H(phi)"=>(interp.H ∘ φh),
-        "|nabla(phi))|"=>(norm ∘ ∇(φh)),
+        "|nabla(phi)|"=>(norm ∘ ∇(φh)),
         "uh1"=>uh[1],
         "uh2"=>uh[2],
         "uh3"=>uh[3],

Deprecated/Deprecated_scripts/AD_AM_testing.jl

@@ -1,4 +1,4 @@
-using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LSTO_Distributed
+using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LevelSetTopOpt
 
 """
   ...
@@ -122,13 +122,13 @@ function main()
   #   print_history(it,["J"=>Ji])
   #   write_history(history,path*"/history.csv")
   #   uhi = get_state(pcfs)
-  #   write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh))];iter_mod=1)
+  #   write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh))];iter_mod=1)
   # end
   # it,Ji,_,_ = last(optimiser.history)
   # print_history(it,["J"=>Ji])
   # write_history(optimiser.history,path*"/history.csv")
   # uhi = get_state(pcfs)
-  # write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh))];iter_mod=1)
+  # write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh))];iter_mod=1)
 
   @show J_val
 

Deprecated/Deprecated_scripts/inverter_AD_testing.jl

@@ -1,4 +1,4 @@
-using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LSTO_Distributed
+using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LevelSetTopOpt
 
 """
   (Serial) Inverter mechanism with augmented Lagrangian method in 2D.

Deprecated/Deprecated_scripts/main_inverter_(Based on Laurain).jl

@@ -1,4 +1,4 @@
-using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LSTO_Distributed
+using Gridap, GridapDistributed, GridapPETSc, PartitionedArrays, LevelSetTopOpt
 
 """
   (Serial) Inverter mechanism with augmented Lagrangian method in 2D.
@@ -99,14 +99,14 @@ function main()
     print_history(it,["J"=>Ji,"C"=>Ci,"L"=>Li,"λ"=>λi,"Λ"=>Λi])
     write_history(history,path*"/history.csv")
     # uhi = get_state(pcfs)
-    # write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh)),"uh"=>uhi];iter_mod=1)
+    # write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh)),"uh"=>uhi];iter_mod=1)
   end
   it,Ji,Ci,Li = last(optimiser.history)
   λi = optimiser.λ; Λi = optimiser.Λ
   print_history(it,["J"=>Ji,"C"=>Ci,"L"=>Li,"λ"=>λi,"Λ"=>Λi])
   write_history(optimiser.history,path*"/history.csv")
   uhi = get_state(pcfs)
-  write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh)),"uh"=>uhi];iter_mod=1)
+  write_vtk(Ω,path*"/struc_$it",it,["phi"=>φh,"H(phi)"=>(H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh)),"uh"=>uhi];iter_mod=1)
 end
 
 main();

Deprecated/auto_diff_elastic_compliance_serial.jl

@@ -200,7 +200,7 @@ hilb_rel_error = (abs(dϕh_Ω-v_J_Ω))/abs(v_J_Ω)
 path = dirname(dirname(@__DIR__))*"/results/AutoDiffTesting";
 writevtk(Ω,path,cellfields=["phi"=>φh,
     "H(phi)"=>(interp.H ∘ φh),
-    "|nabla(phi))|"=>(norm ∘ ∇(φh)),
+    "|nabla(phi)|"=>(norm ∘ ∇(φh)),
     "uh"=>uh,
     "J′_abs_error"=>abs_error,
     "J′_rel_error"=>rel_error,

Deprecated/elastic_compliance_for_jordi.jl

@@ -32,7 +32,7 @@ function main(mesh_partition,distribute)
         φh = interpolate(x->-sqrt((x[1]-0.5)^2+(x[2]-0.5)^2+(x[3]-0.5)^2)+0.25,V_φ)
         J,v_J,uh = elastic_compliance(φh,g,C,solve_data,interp,t)
         display("Objective = $J")
-        writevtk(Ω,path,cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh)),"uh"=>uh])
+        writevtk(Ω,path,cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh)),"uh"=>uh])
     end
     t
 end

Deprecated/test_periodic_finitediff.jl

@@ -157,4 +157,4 @@ v = get_free_dof_values(vh)
 advect!(φ,v,model,Δ,γ,50)
 reinit!(φ,model,Δ,0.5,2000,reinit_tol)
 
-writevtk(Ω,(@__DIR__)*"\\Results\\test_reinit_2d_plus_advect",cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh))]);
+writevtk(Ω,(@__DIR__)*"\\Results\\test_reinit_2d_plus_advect",cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh))]);

Deprecated/tests_solver.jl

@@ -117,7 +117,7 @@ function main(mesh_partition,distribute)
         solver = ElasticitySolver(solve_data.V)
         J,v_J,uh = elastic_compliance(φh,g,C,solve_data,interp,t,solver)
         display("Objective = $J")
-        writevtk(Ω,path,cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi))|"=>(norm ∘ ∇(φh)),"uh"=>uh])
+        writevtk(Ω,path,cellfields=["phi"=>φh,"H(phi)"=>(interp.H ∘ φh),"|nabla(phi)|"=>(norm ∘ ∇(φh)),"uh"=>uh])
     end
     t
 end

Deprecated/tests_solver2_mpi.jl

@@ -12,7 +12,7 @@ import GridapDistributed.DistributedDiscreteModel
 import GridapDistributed.DistributedMeasure
 import GridapDistributed.DistributedTriangulation
 
-using LSTO_Distributed
+using LevelSetTopOpt
 
 function isotropic_3d(E::M,nu::M) where M<:AbstractFloat
     λ = E*nu/((1+nu)*(1-2nu)); μ = E/(2*(1+nu))

Project.toml

@@ -1,4 +1,4 @@
-name = "LSTO_Distributed"
+name = "LevelSetTopOpt"
 uuid = "27dd0110-1916-4fd6-8b4b-1bc109db1170"
 authors = ["Zach Wegert <[email protected]>", "JordiManyer <[email protected]>"]
 version = "0.1.0"
@@ -24,7 +24,7 @@ PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [extras]
 MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"