Start new project Tesserae.jl

.github/workflows/CI.yml

@@ -81,6 +81,6 @@ jobs:
         shell: julia --project=docs --color=yes {0}
         run: |
           using Documenter: DocMeta, doctest
-          using Sequoia
-          DocMeta.setdocmeta!(Sequoia, :DocTestSetup, :(using Sequoia); recursive=true)
-          doctest(Sequoia)
+          using Tesserae
+          DocMeta.setdocmeta!(Tesserae, :DocTestSetup, :(using Tesserae); recursive=true)
+          doctest(Tesserae)

Project.toml

@@ -1,5 +1,5 @@
-name = "Sequoia"
-uuid = "30a04e26-4a89-4862-aa00-4d71e820c402"
+name = "Tesserae"
+uuid = "fd374396-9d9c-4d88-9aa5-37a7f6105aca"
 authors = ["Keita Nakamura <keita.nakamura.1109@gmail.com>"]
 version = "0.3.0"
 

README.md

@@ -1,6 +1,6 @@
-# Sequoia.jl
+# Tesserae.jl
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://KeitaNakamura.github.io/Sequoia.jl/stable)
-[![Develop](https://img.shields.io/badge/docs-dev-blue.svg)](https://KeitaNakamura.github.io/Sequoia.jl/dev)
-[![CI](https://github.com/KeitaNakamura/Sequoia.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/KeitaNakamura/Sequoia.jl/actions/workflows/CI.yml)
-[![codecov](https://codecov.io/gh/KeitaNakamura/Sequoia.jl/graph/badge.svg?token=bD5urvSTeq)](https://codecov.io/gh/KeitaNakamura/Sequoia.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://KeitaNakamura.github.io/Tesserae.jl/stable)
+[![Develop](https://img.shields.io/badge/docs-dev-blue.svg)](https://KeitaNakamura.github.io/Tesserae.jl/dev)
+[![CI](https://github.com/KeitaNakamura/Tesserae.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/KeitaNakamura/Tesserae.jl/actions/workflows/CI.yml)
+[![codecov](https://codecov.io/gh/KeitaNakamura/Tesserae.jl/graph/badge.svg?token=H5BHWIIBTG)](https://codecov.io/gh/KeitaNakamura/Tesserae.jl)

docs/Project.toml

@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-Sequoia = "30a04e26-4a89-4862-aa00-4d71e820c402"
+Tesserae = "fd374396-9d9c-4d88-9aa5-37a7f6105aca"

docs/literate/examples/dam_break.jl

@@ -2,7 +2,7 @@
 
 # ## Main function
 
-using Sequoia
+using Tesserae
 using LinearAlgebra
 
 abstract type Transfer end
@@ -115,7 +115,7 @@ function main(transfer::Transfer = FLIP(1.0))
     fps = 30
     savepoints = collect(LinRange(t, T, round(Int, T*fps)+1))
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         ## Update interpolation values based on the nodes of active cells
         ## where the particles are located
@@ -257,8 +257,8 @@ function variational_multiscale_method(state)
 
         ## Solve nonlinear system
         U = zeros(ndofs(dofmap)) # Initialize nodal dispacement and pressure with zero
-        solved = Sequoia.newton!(U, U->residual(U,state), U->J;
-                                 linsolve=(x,A,b)->ldiv!(x,A,b), atol=1e-10, rtol=1e-10)
+        solved = Tesserae.newton!(U, U->residual(U,state), U->J;
+                                  linsolve=(x,A,b)->ldiv!(x,A,b), atol=1e-10, rtol=1e-10)
 
         ## If the simulation fails to solve, retry with a smaller time step
         solved || (Δt /= 2)

docs/literate/examples/elastic_impact.jl

@@ -13,7 +13,7 @@
 # [^4]: [Li, X., Fang, Y., Li, M. and Jiang, C., 2022. BFEMP: Interpenetration-free MPM–FEM coupling with barrier contact. Computer Methods in Applied Mechanics and Engineering, 390, p.114350.](https://doi.org/10.1016/j.cma.2021.114350)
 #
 
-using Sequoia
+using Tesserae
 
 abstract type Transfer end
 struct FLIP <: Transfer α::Float64 end
@@ -106,7 +106,7 @@ function main(transfer::Transfer = FLIP(1.0))
     fps = 120
     savepoints = collect(LinRange(t, T, round(Int, T*fps)+1))
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         ## Calculate timestep based on the wave speed
         vmax = maximum(@. sqrt((λ+2μ) / (particles.m/particles.V)) + norm(particles.v))

docs/literate/examples/implicit_jacobian_based.jl

@@ -1,6 +1,6 @@
 # # Jacobian-based implicit method
 
-using Sequoia
+using Tesserae
 
 function main()
 
@@ -56,7 +56,7 @@ function main()
     grid = generate_grid(GridProp, CartesianMesh(h, (0.0,1.2), (0.0,2.0), (-0.2,0.2)))
 
     ## Particles
-    beam = Sequoia.Box((0,1), (0.85,1.15), (-0.15,0.15))
+    beam = Tesserae.Box((0,1), (0.85,1.15), (-0.15,0.15))
     particles = generate_particles(ParticleProp, grid.X; domain=beam, alg=GridSampling())
     particles.V⁰ .= volume(beam) / length(particles)
     @. particles.m = ρ⁰ * particles.V⁰
@@ -87,7 +87,7 @@ function main()
     t = 0.0
     step = 0
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         for p in eachindex(particles, mpvalues)
             update!(mpvalues[p], particles.x[p], grid.X)
@@ -122,7 +122,7 @@ function main()
         U = copy(dofmap(grid.u)) # Convert grid data to plain vector data
         compute_residual(U) = residual(U, state)
         compute_jacobian(U) = jacobian(U, state)
-        Sequoia.newton!(U, compute_residual, compute_jacobian)
+        Tesserae.newton!(U, compute_residual, compute_jacobian)
 
         ## Grid dispacement, velocity and acceleration have been updated during Newton's iterations
         @G2P grid=>i particles=>p mpvalues=>ip begin

docs/literate/examples/implicit_jacobian_free.jl

@@ -1,6 +1,6 @@
 # # Jacobian-free Newton--Krylov method
 
-using Sequoia
+using Tesserae
 
 using IterativeSolvers: gmres!
 using LinearMaps: LinearMap
@@ -59,7 +59,7 @@ function main()
     grid = generate_grid(GridProp, CartesianMesh(h, (0.0,1.2), (0.0,2.0), (-0.2,0.2)))
 
     ## Particles
-    beam = Sequoia.Box((0,1), (0.85,1.15), (-0.15,0.15))
+    beam = Tesserae.Box((0,1), (0.85,1.15), (-0.15,0.15))
     particles = generate_particles(ParticleProp, grid.X; domain=beam, alg=GridSampling())
     particles.V⁰ .= volume(beam) / length(particles)
     @. particles.m = ρ⁰ * particles.V⁰
@@ -86,7 +86,7 @@ function main()
     t = 0.0
     step = 0
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         for p in eachindex(particles, mpvalues)
             update!(mpvalues[p], particles.x[p], grid.X)
@@ -121,7 +121,7 @@ function main()
         U = copy(dofmap(grid.u)) # Convert grid data to plain vector data
         compute_residual(U) = residual(U, state)
         compute_jacobian(U) = jacobian(U, state)
-        Sequoia.newton!(U, compute_residual, compute_jacobian; linsolve = (x,A,b)->gmres!(x,A,b))
+        Tesserae.newton!(U, compute_residual, compute_jacobian; linsolve = (x,A,b)->gmres!(x,A,b))
 
         ## Grid dispacement, velocity and acceleration have been updated during Newton's iterations
         @G2P grid=>i particles=>p mpvalues=>ip begin

docs/literate/examples/rigid_body_contact.jl

@@ -1,6 +1,6 @@
 # # Frictional contact with rigid body
 
-using Sequoia
+using Tesserae
 
 mutable struct Disk{dim, T}
     x::Vec{dim, T}
@@ -109,7 +109,7 @@ function main()
     fps = 20
     savepoints = collect(LinRange(t, T, round(Int, T*fps)+1))
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         vmax = maximum(@. sqrt((λ+2G) / (particles.m/particles.V)) + norm(particles.v))
         Δt = CFL * spacing(grid) / vmax

docs/literate/examples/tlmpm_vortex.jl

@@ -8,7 +8,7 @@
 #
 # [^1]: [de Vaucorbeil, A., Nguyen, V.P. and Hutchinson, C.R., 2020. A Total-Lagrangian Material Point Method for solid mechanics problems involving large deformations. Computer Methods in Applied Mechanics and Engineering, 360, p.112783.](https://doi.org/10.1016/j.cma.2019.112783)
 
-using Sequoia
+using Tesserae
 
 function main()
 
@@ -99,7 +99,7 @@ function main()
     fps = 60
     savepoints = collect(LinRange(t, T, round(Int, T*fps)+1))
 
-    Sequoia.@showprogress while t < T
+    Tesserae.@showprogress while t < T
 
         ## Calculate timestep based on the wave speed
         vmax = maximum(@. sqrt((λ+2μ) / (particles.m/(particles.V⁰ * det(particles.F)))) + norm(particles.v))

docs/make.jl

@@ -1,11 +1,11 @@
 using Documenter
-using Sequoia
+using Tesserae
 
 ENV["PLOTS_TEST"] = "true"
 ENV["GKSwstype"] = "100"
 
 # Setup for doctests in docstrings
-DocMeta.setdocmeta!(Sequoia, :DocTestSetup, :(using Sequoia); recursive=true)
+DocMeta.setdocmeta!(Tesserae, :DocTestSetup, :(using Tesserae); recursive=true)
 
 # generate documentation by Literate.jl
 include("literate.jl")
@@ -14,8 +14,8 @@ makedocs(;
     format = Documenter.HTML(
         prettyurls = get(ENV, "CI", nothing) == "true",
     ),
-    modules = [Sequoia],
-    sitename = "Sequoia.jl",
+    modules = [Tesserae],
+    sitename = "Tesserae.jl",
     pages=[
         "Home" => "index.md",
         "getting_started.md",
@@ -33,6 +33,6 @@ makedocs(;
 )
 
 deploydocs(
-    repo = "github.com/KeitaNakamura/Sequoia.jl.git",
+    repo = "github.com/KeitaNakamura/Tesserae.jl.git",
     devbranch = "main",
 )

docs/src/getting_started.md

@@ -1,7 +1,7 @@
 # Getting Started
 
 ```@example
-using Sequoia
+using Tesserae
 import Plots
 
 # Material constants

docs/src/index.md

@@ -1 +1 @@
-# Sequoia
+# Tesserae

src/Sequoia.jl → src/Tesserae.jl

@@ -1,4 +1,4 @@
-module Sequoia
+module Tesserae
 
 using Base: @propagate_inbounds, @_inline_meta, @_propagate_inbounds_meta
 using Base.Broadcast: Broadcasted, ArrayStyle, DefaultArrayStyle
@@ -96,4 +96,4 @@ include("implicit.jl")
 
 include("vtk.jl")
 
-end # module Sequoia
+end # module Tesserae

src/blockspace.jl

@@ -116,7 +116,7 @@ blocksize(gridsize::Tuple{Vararg{Int}}) = @. (gridsize-1)>>BLOCKFACTOR+1
 blocksize(A::AbstractArray) = blocksize(size(A))
 
 """
-    Sequoia.whichblock(x::Vec, mesh::CartesianMesh)
+    Tesserae.whichblock(x::Vec, mesh::CartesianMesh)
 
 Return block index where `x` locates.
 The unit block size is `2^$BLOCKFACTOR` cells.
@@ -137,7 +137,7 @@ julia> mesh = CartesianMesh(1, (0,10), (0,10))
  [9.0, 0.0]   [9.0, 1.0]   [9.0, 2.0]      [9.0, 9.0]   [9.0, 10.0]
  [10.0, 0.0]  [10.0, 1.0]  [10.0, 2.0]  …  [10.0, 9.0]  [10.0, 10.0]
 
-julia> Sequoia.whichblock(Vec(8.5, 1.5), mesh)
+julia> Tesserae.whichblock(Vec(8.5, 1.5), mesh)
 CartesianIndex(2, 1)
 ```
 """

src/implicit.jl

@@ -134,11 +134,11 @@ function P2G_Matrix_macro(schedule::QuoteNode, grid_pair, particles_pair, mpvalu
         globalname = lhs.args[1]
         localname = gensym(globalname)
 
-        Meta.isexpr(ex, :(=)) && push!(init_global_matrices, :(Sequoia.fillzero!($globalname)))
+        Meta.isexpr(ex, :(=)) && push!(init_global_matrices, :(Tesserae.fillzero!($globalname)))
         push!(global_matrices, globalname)
         push!(create_local_matrices, :($localname = Array{eltype($globalname)}(undef, length($localdofs), length($localdofs))))
         push!(assemble_local_matrices, :(@inbounds $localname[$I,$J] .= $trySArray($rhs))) # converting `Tensor` to `SArray` is faster for setindex!
-        push!(add_local_to_global, :(Sequoia.add!($globalname, $dofs, $dofs, $localname)))
+        push!(add_local_to_global, :(Tesserae.add!($globalname, $dofs, $dofs, $localname)))
         push!(assertions, :(@assert $globalname isa AbstractMatrix && size($globalname, 1) == size($globalname, 2)))
     end
     push!(assertions, :(@assert allequal($([:(size($m)) for m in global_matrices]...,))))
@@ -150,7 +150,7 @@ function P2G_Matrix_macro(schedule::QuoteNode, grid_pair, particles_pair, mpvalu
         @assert Meta.isexpr(lhs, :ref) && all(lhs.args[2:end] .== i) # currently support only `A[i,i] = ...`
         complete_parent_from_index!(ex.args[2], [grid=>i])
         globalname = lhs.args[1]
-        push!(grid_sums, :(Sequoia.add!($globalname, $I, $I, $(ex.args[2]))))
+        push!(grid_sums, :(Tesserae.add!($globalname, $I, $I, $(ex.args[2]))))
     end
 
     body = quote

src/particles.jl

@@ -66,15 +66,15 @@ end
 
 function _generate_points(::Type{ParticleProp}, mesh::CartesianMesh{dim, T}, spacing::Real, alg::SamplingAlgorithm, ::Nothing) where {ParticleProp, dim, T}
     domain = tuple.(Tuple(first(mesh)), Tuple(last(mesh)))
-    point_sampling(alg, Sequoia.spacing(mesh) * T(spacing), domain...)
+    point_sampling(alg, Tesserae.spacing(mesh) * T(spacing), domain...)
 end
 function _generate_points(::Type{ParticleProp}, mesh::CartesianMesh{dim, T}, spacing::Real, alg::GridSampling, box::Box) where {ParticleProp, dim, T}
     domain = tuple.(Tuple(first(mesh)), Tuple(last(mesh)))
-    points = point_sampling(alg, Sequoia.spacing(mesh) * T(spacing), domain...)
+    points = point_sampling(alg, Tesserae.spacing(mesh) * T(spacing), domain...)
     filter(x -> isinside(x, box), points)
 end
 function _generate_points(::Type{ParticleProp}, mesh::CartesianMesh{dim, T}, spacing::Real, alg::PoissonDiskSampling, box::Box) where {ParticleProp, dim, T}
-    points = point_sampling(alg, Sequoia.spacing(mesh) * T(spacing), box.domain...)
+    points = point_sampling(alg, Tesserae.spacing(mesh) * T(spacing), box.domain...)
 end
 
 function _reorder_particles!(particles::AbstractVector, mesh::CartesianMesh)

src/sparray.jl

@@ -116,10 +116,10 @@ julia> A[1,1] # still zero
 
 This is because the block where index `(1,1)` is located is not activated yet.
 To activate the block, update sparsity pattern by `update_block_sparsity!(A, spy)`
-where `spy` must have `Sequoia.blocksize(A)`.
+where `spy` must have `Tesserae.blocksize(A)`.
 
 ```jldoctest sparray
-julia> spy = trues(Sequoia.blocksize(A))
+julia> spy = trues(Tesserae.blocksize(A))
 1×1 BitMatrix:
  1
 

src/transfer.jl

@@ -75,7 +75,7 @@ function P2G_sum_macro(schedule::QuoteNode, grid_pair, particles_pair, mpvalues_
         # `lhs` is, for example, `grid.m[i]`
         lhs = ex.args[1]
         if Meta.isexpr(ex, :(=))
-            push!(init_gridprops, :(Sequoia.fillzero!($(lhs.args[1]))))
+            push!(init_gridprops, :(Tesserae.fillzero!($(lhs.args[1]))))
         end
         push!(sum_names, lhs.args[1].args[2].value) # extract `m` for `grid.m[i]`
     end
@@ -107,7 +107,7 @@ function P2G_expr(schedule::QuoteNode, grid, particles, mpvalues, space, p, body
     if isnothing(space)
         body = quote
             $(schedule.value != :nothing) && @warn "@P2G: `BlockSpace` must be given for threaded computation" maxlog=1
-            for $p in Sequoia.eachparticleindex($particles, $mpvalues)
+            for $p in Tesserae.eachparticleindex($particles, $mpvalues)
                 $body
             end
         end
@@ -122,7 +122,7 @@ function P2G_expr(schedule::QuoteNode, grid, particles, mpvalues, space, p, body
             body = :(@threaded $schedule $body)
         end
         body = quote
-            for $blocks in Sequoia.threadsafe_blocks($space)
+            for $blocks in Tesserae.threadsafe_blocks($space)
                 $body
             end
         end
@@ -140,7 +140,7 @@ function P2G_nosum_macro(schedule, grid_pair, nosum_equations::Vector)
     foreach(ex->findarrays_from_index!(vars, i, ex), nosum_equations)
 
     body = quote
-        Sequoia.foreach_gridindex(Val($schedule), Sequoia.GridIndexStyle($(vars...)), $grid) do $i
+        Tesserae.foreach_gridindex(Val($schedule), Tesserae.GridIndexStyle($(vars...)), $grid) do $i
             Base.@_inline_meta
             $(nosum_equations...)
         end
@@ -244,7 +244,7 @@ function G2P_macro(schedule::QuoteNode, grid_pair, particles_pair, mpvalues_pair
     if isallunderscore(mpvalues)
         iterator = :(eachindex($particles))
     else
-        iterator = :(Sequoia.eachparticleindex($particles, $mpvalues))
+        iterator = :(Tesserae.eachparticleindex($particles, $mpvalues))
     end
 
     if schedule.value == :nothing

test/LocalPreferences.toml

@@ -1,4 +1,4 @@
-[Sequoia]
+[Tesserae]
 debug_mode = true
 block_factor = 3
 threaded_macro = true

test/Project.toml

@@ -3,5 +3,5 @@ IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Sequoia = "30a04e26-4a89-4862-aa00-4d71e820c402"
+Tesserae = "fd374396-9d9c-4d88-9aa5-37a7f6105aca"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/blockspace.jl

@@ -5,13 +5,13 @@
         (x-1.5)^2 + (y-2)^2 < 1
     end
     blockspace = (@inferred BlockSpace(mesh))
-    @test size(blockspace) === Sequoia.blocksize(mesh)
+    @test size(blockspace) === Tesserae.blocksize(mesh)
     @test all(isempty, blockspace)
     @test typeof(blockspace[1]) === eltype(blockspace)
     update!(blockspace, xₚ)
-    ptsinblks = map(_->Int[], CartesianIndices(Sequoia.blocksize(mesh)))
+    ptsinblks = map(_->Int[], CartesianIndices(Tesserae.blocksize(mesh)))
     for p in eachindex(xₚ)
-        I = Sequoia.whichblock(xₚ[p], mesh)
+        I = Tesserae.whichblock(xₚ[p], mesh)
         I === nothing || push!(ptsinblks[I], p)
     end
     @test blockspace == ptsinblks