Merge pull request #76 from gridap/adds_algoim_interface

Adds algoim interface

.github/workflows/ci.yml

@@ -70,6 +70,41 @@ jobs:
       - run: |
           julia --color=yes --project=. --check-bounds=yes --depwarn=error -e '
             (1,) .== 1; include("test/GridapEmbeddedTests/runtests.jl")'
+  algoimutils:
+    name: AlgoimUtils ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.8'
+        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
+      - run: |
+          julia --color=yes --project=. --check-bounds=yes --depwarn=error -e '
+            using Pkg; Pkg.instantiate()'
+      - run: |
+          julia --color=yes --project=. --check-bounds=yes --depwarn=error -e '
+            (1,) .== 1; include("test/AlgoimUtilsTests/runtests.jl")'
   docs:
     name: Documentation
     runs-on: ubuntu-latest

LICENSE.md

@@ -1,7 +1,7 @@
 GridapEmbedded.jl Copyright and License
 ==
 
-Copyright (c) 2020 by [Francesc Verdugo](mailto:[email protected]) and [Santiago Badia](mailto:[email protected]).
+Copyright (c) 2020 by [Francesc Verdugo](mailto:[email protected]), [Eric Neiva](mailto:[email protected]) and [Santiago Badia](mailto:[email protected]).
 
 GridapEmbedded.jl is licensed under the MIT Expat License
 
@@ -28,19 +28,33 @@ SOFTWARE.
 Citing `Gridap`
 ==
 
-In order to give credit to the `Gridap` contributors, we simply ask you to cite the refence below in any publication in which you have made use of `Gridap` packages.
-
-F. Verdugo and S. Badia. *A user-guide to Gridap -- grid-based approximation of partial differential equations in Julia*, 2019. [arXiv:1910.01412](https://arxiv.org/abs/1910.01412)
+In order to give credit to the `Gridap` contributors, we simply ask you to cite the references below in any publication in which you have made use of `Gridap` packages.
 
 ```
-@article{gridap_guide_2019,
-    author={Francesc Verdugo and Santiago Badia},
-    journal = {{arXiv}},
-    title = {{A user-guide to Gridap -- grid-based approximation of partial differential equations in Julia}},
-    year = {2019},
-    eprint={1910.01412},
-    archivePrefix={arXiv},
-    primaryClass={cs.MS},
+@article{Badia2020,
+  doi = {10.21105/joss.02520},
+  url = {https://doi.org/10.21105/joss.02520},
+  year = {2020},
+  publisher = {The Open Journal},
+  volume = {5},
+  number = {52},
+  pages = {2520},
+  author = {Santiago Badia and Francesc Verdugo},
+  title = {Gridap: An extensible Finite Element toolbox in Julia},
+  journal = {Journal of Open Source Software}
+}
+
+@article{Verdugo2022,
+  doi = {10.1016/j.cpc.2022.108341},
+  url = {https://doi.org/10.1016/j.cpc.2022.108341},
+  year = {2022},
+  month = jul,
+  publisher = {Elsevier {BV}},
+  volume = {276},
+  pages = {108341},
+  author = {Francesc Verdugo and Santiago Badia},
+  title = {The software design of Gridap: A Finite Element package based on the Julia {JIT} compiler},
+  journal = {Computer Physics Communications}
 }
 ```
 
@@ -92,4 +106,4 @@ By making a contribution to this project, I certify that:
 Contact
 ==
 
-Please, contact the project administrators, [Santiago Badia](mailto:[email protected]) and [Francesc Verdugo](mailto:[email protected].edu), for further questions about licenses and terms of use.
+Please, contact the project administrators, [Francesc Verdugo](mailto:[email protected]), [Eric Neiva](mailto:[email protected]) and [Santiago Badia](mailto:santiago.badia@monash.edu), for further questions about licenses and terms of use.

NEWS.md

@@ -4,7 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.8.3] - 2024-08-02
+## [0.9.0] - 2024-01-22
+
+### Added
+- Interface to Algoim v0.2, which provides algoim's high-order quadrature algorithms for domains implicitly-defined by multivariate polynomials and high-order accurate algorithms for computing closest points on implicitly-defined surfaces. Since PR [#76](https://github.com/gridap/GridapEmbedded.jl/pull/76).
+
+## [0.8.3] - 2024-01-02
 
 ### Added
 - Support for FillArrays v1. Since PR [#75](https://github.com/gridap/GridapEmbedded.jl/pull/75).

Project.toml

@@ -1,18 +1,21 @@
 name = "GridapEmbedded"
 uuid = "8838a6a3-0006-4405-b874-385995508d5d"
-authors = ["Francesc Verdugo <[email protected].edu>"]
-version = "0.8.3"
+authors = ["Francesc Verdugo <[email protected]>", "Eric Neiva <[email protected]>", "Santiago Badia <santiago.badia@monash.edu>"]
+version = "0.9.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+Algoim = "0eb9048c-21de-4c7a-bfac-056de1940b74"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
+CxxWrap = "1f15a43c-97ca-5a2a-ae31-89f07a497df4"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Gridap = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MiniQhull = "978d7f02-9e05-4691-894f-ae31a51d76ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+algoimWrapper_jll = "3c43aa7b-5398-51f3-8d75-8f051e6faa4d"
 
 [compat]
 AbstractTrees = "0.3.3, 0.4"

docs/make.jl

@@ -8,7 +8,7 @@ makedocs(;
     ],
     repo="https://github.com/gridap/GridapEmbedded.jl/blob/{commit}{path}#L{line}",
     sitename="GridapEmbedded.jl",
-    authors="Francesc Verdugo <[email protected].edu>",
+    authors="Francesc Verdugo <[email protected]>, Eric Neiva <[email protected]> and Santiago Badia <santiago.badia@monash.edu>",
 )
 
 deploydocs(;

src/AgFEM/AgFEM.jl

@@ -18,6 +18,7 @@ using GridapEmbedded.Interfaces: compute_subcell_to_inout
 
 export aggregate
 export color_aggregates
+export aggregate_narrow_band
 export AggregateAllCutCells
 export compute_cell_bboxes
 export compute_cell_to_dface_bboxes

src/AgFEM/AggregateBoundingBoxes.jl

@@ -19,6 +19,18 @@ function init_bboxes(cell_to_coords,cut::EmbeddedDiscretization;in_or_out=IN)
   bgcell_to_cbboxes
 end
 
+function init_bboxes(cell_to_coords,cut_measure::Measure)
+  bgcell_to_cbboxes = init_bboxes(cell_to_coords)
+  quad = get_cell_quadrature(cut_measure)
+  trian = get_triangulation(quad)
+  model = get_active_model(trian)
+  ccell_to_bgcell = get_cell_to_parent_cell(model)
+  for (cc,bc) in enumerate(ccell_to_bgcell)
+    bgcell_to_cbboxes[bc] = compute_subcell_bbox(quad.cell_point[cc])
+  end
+  bgcell_to_cbboxes
+end
+
 function init_cut_bboxes(cut,ccell_to_bgcell,in_or_out)
   subcell_to_inout   = compute_subcell_to_inout(cut,cut.geo)
   subcell_is_in      = lazy_map(i->i==in_or_out,subcell_to_inout)

src/AgFEM/CellAggregation.jl

@@ -303,3 +303,60 @@ function _color_aggregates_barrier(cell_to_cellin,cell_to_faces,face_to_cells)
 
   cell_to_color
 end
+
+# Specialised methods for Algoim quadratures
+
+function aggregate(bgtrian,cell_to_is_active,cell_to_is_cut,in_or_out)
+  n_cells = length(cell_to_is_active)
+  @assert n_cells == length(cell_to_is_cut)
+
+  cell_to_unit_cut_meas = lazy_map(cell_to_is_active,cell_to_is_cut) do isa, isc
+    !isa ? 0.0 : (isc ? 0.0 : 1.0)
+  end
+
+  cell_to_inoutcut = lazy_map(cell_to_is_active,cell_to_is_cut) do isa, isc
+    !isa ? OUT : (isc ? CUT : IN)
+  end
+
+  cell_to_coords = get_cell_coordinates(bgtrian)
+  model = get_background_model(bgtrian)
+  topo = get_grid_topology(model)
+  D = num_cell_dims(model)
+  cell_to_faces = get_faces(topo,D,D-1)
+  face_to_cells = get_faces(topo,D-1,D)
+  # A hack follows to avoid constructing the actual facet_to_inoutcut array
+  facet_to_inoutcut = fill(in_or_out,num_faces(model,D-1)) 
+
+  threshold = 1.0
+  _aggregate_by_threshold_barrier(
+    threshold,cell_to_unit_cut_meas,facet_to_inoutcut,cell_to_inoutcut,
+    in_or_out,cell_to_coords,cell_to_faces,face_to_cells)
+end
+
+function aggregate_narrow_band(bgtrian,cell_to_is_in_narrow,cell_to_is_active,cell_to_is_cut,in_or_out)
+  n_cells = length(cell_to_is_in_narrow)
+  @assert n_cells == length(cell_to_is_active)
+  @assert n_cells == length(cell_to_is_cut)
+
+  cell_to_unit_cut_meas = lazy_map(cell_to_is_active,cell_to_is_cut) do isa, isc
+    ( isa & !isc ) ? 1.0 : 0.0
+  end
+
+  cell_to_inoutcut = lazy_map(cell_to_is_in_narrow,cell_to_is_active,cell_to_is_cut) do isn, isa, isc
+    !isn ? OUT : ( ( isa & !isc ) ? IN : CUT )
+  end
+
+  cell_to_coords = get_cell_coordinates(bgtrian)
+  model = get_background_model(bgtrian)
+  topo = get_grid_topology(model)
+  D = num_cell_dims(model)
+  cell_to_faces = get_faces(topo,D,D-1)
+  face_to_cells = get_faces(topo,D-1,D)
+  # A hack follows to avoid constructing the actual facet_to_inoutcut array
+  facet_to_inoutcut = fill(in_or_out,num_faces(model,D-1)) 
+
+  threshold = 1.0
+  _aggregate_by_threshold_barrier(
+    threshold,cell_to_unit_cut_meas,facet_to_inoutcut,cell_to_inoutcut,
+    in_or_out,cell_to_coords,cell_to_faces,face_to_cells)
+end