Compute local rank grid with lazy_grid

.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/format_check.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.9'
+          - '1.10'
         os:
           - ubuntu-latest
         arch:

_typos.toml

@@ -0,0 +1,3 @@
+[default.extend-words]
+Ths = "Ths"
+oly = "oly"

miniapps/benchmarks/stokes2D/RunStokesBench2D.jl

@@ -3,7 +3,7 @@ using MPI: MPI
 using GLMakie
 
 # setup ParallelStencil.jl environment
-model = PS_Setup(:cpu, Float64, 2)
+model = PS_Setup(:cpu, Float64, 2) # :cpu | :CUDA | :AMDGPU
 environment!(model)
 
 # choose benchmark
@@ -16,13 +16,13 @@ nx, ny = 64, 64
 finalize_MPI = false
 
 # :single for a single run model with nx, ny resolution
-# :multiple for grid sensitivy error plot
+# :multiple for grid sensitivity error plot
 runtype = :single
 
 if benchmark == :solcx
     # benchmark reference:
     # Duretz, Thibault, et al. "Discretization errors and free surface stabilization
-    # in the finite difference and marker‐in‐cell method for applied geodynamics: 
+    # in the finite difference and marker‐in‐cell method for applied geodynamics:
     # A numerical study." Geochemistry, Geophysics, Geosystems 12.7 (2011).
     # DOI: 10.1029/2011GC003567
 
@@ -51,7 +51,7 @@ if benchmark == :solcx
 elseif benchmark == :solkz
     # benchmark reference:
     # Duretz, Thibault, et al. "Discretization errors and free surface stabilization
-    # in the finite difference and marker‐in‐cell method for applied geodynamics: 
+    # in the finite difference and marker‐in‐cell method for applied geodynamics:
     # A numerical study." Geochemistry, Geophysics, Geosystems 12.7 (2011).
     # DOI: 10.1029/2011GC003567
 

miniapps/benchmarks/stokes2D/VanKeken.jl/VanKeken.jl

@@ -7,11 +7,11 @@ backend = "CUDA_Float64_2D" # options: "CUDA_Float64_2D" "Threads_Float64_2D"
 # set_backend(backend) # run this on the REPL to switch backend
 
 # setup ParallelStencil.jl environment
-@static if occursin("CUDA", JustPIC.backend) 
+@static if occursin("CUDA", JustPIC.backend)
     model  = PS_Setup(:CUDA, Float64, 2)
     environment!(model)
 else
-    model  = PS_Setup(:Threads, Float64, 2)
+    model  = PS_Setup(:cpu, Float64, 2)
     environment!(model)
 end
 
@@ -107,14 +107,15 @@ end
 function main2D(igg; ny=16, nx=ny*8, figdir="model_figs")
 
     # Physical domain ------------------------------------
-    ly       = 1            # domain length in y
-    lx       = ly           # domain length in x
-    ni       = nx, ny       # number of cells
-    li       = lx, ly       # domain length in x- and y-
-    di       = @. li / ni   # grid step in x- and -y
-    origin   = 0.0, 0.0     # origin coordinates
-    xci, xvi = lazy_grid(di, li, ni; origin=origin) # nodes at the center and vertices of the cells
-    dt       = Inf
+    ly           = 1            # domain length in y
+    lx           = ly           # domain length in x
+    ni           = nx, ny       # number of cells
+    li           = lx, ly       # domain length in x- and y-
+    di           = @. li / ni   # grid step in x- and -y
+    origin       = 0.0, 0.0     # origin coordinates
+    grid         = Geometry(ni, li; origin = origin)
+    (; xci, xvi) = grid # nodes at the center and vertices of the cells
+    dt           = Inf
 
     # Physical properties using GeoParams ----------------
     rheology = (
@@ -167,10 +168,12 @@ function main2D(igg; ny=16, nx=ny*8, figdir="model_figs")
     )
 
     # Boundary conditions
-    flow_bcs             = FlowBoundaryConditions(; 
+    flow_bcs             = FlowBoundaryConditions(;
         free_slip = (left =  true, right =  true, top = false, bot = false),
         no_slip   = (left = false, right = false, top =  true, bot =  true),
-    ) 
+    )
+    flow_bcs!(stokes, flow_bcs)
+    update_halo!(stokes.V.Vx, stokes.V.Vy)
 
     # IO ----- -------------------------------------------
     # if it does not exist, make folder where figures are stored

miniapps/benchmarks/stokes2D/elastic_buildup/Elastic_BuildUp.jl

@@ -29,12 +29,13 @@ function elastic_buildup(;
     # Here, we only explicitly store local sizes, but for some applications
     # concerned with strong scaling, it might make more sense to define global sizes,
     # independent of (MPI) parallelization
-    ni        = nx, ny # number of nodes in x- and y-
-    li        = lx, ly  # domain length in x- and y-
-    di        = @. li / ni # grid step in x- and -y
-    igg       = IGG(init_global_grid(nx, ny, 1; init_MPI=init_MPI)...) # init MPI
-    origin    = 0.0, 0.0
-    xci, xvi  = lazy_grid(di, li, ni; origin=origin) # nodes at the center and vertices of the cells
+    ni           = nx, ny # number of nodes in x- and y-
+    li           = lx, ly  # domain length in x- and y-
+    di           = @. li / ni # grid step in x- and -y
+    igg          = IGG(init_global_grid(nx, ny, 1; init_MPI=init_MPI)...) # init MPI
+    origin       = 0.0, 0.0
+    grid         = Geometry(ni, li; origin = origin)
+    (; xci, xvi) = grid # nodes at the center and vertices of the cells
 
     ## (Physical) Time domain and discretization
     yr        = 365.25 * 3600 * 24
@@ -59,12 +60,13 @@ function elastic_buildup(;
         free_slip = (left = true, right = true, top = true, bot = true)
     )
     flow_bcs!(stokes, flow_bcs)
+    update_halo!(stokes.V.Vx, stokes.V.Vy)
 
     # Physical time loop
     t         = 0.0
     it        = 0
     ρg        = @zeros(ni...), @ones(size(stokes.P)) .* g
-    av_τyy    = Float64[] 
+    av_τyy    = Float64[]
     sol_τyy   = Float64[]
     tt        = Float64[]
     local iters

miniapps/benchmarks/stokes2D/elastic_buildup/Elastic_BuildUp_phases_incompressible.jl

@@ -29,22 +29,23 @@ end
 function main(igg; nx=64, ny=64, figdir="model_figs")
 
     # Physical domain ------------------------------------
-    ly = 1e0          # domain length in y
-    lx = ly           # domain length in x
-    ni = nx, ny       # number of cells
-    li = lx, ly       # domain length in x- and y-
-    di = @. li / ni   # grid step in x- and -y
-    origin = 0.0, 0.0     # origin coordinates
-    xci, xvi = lazy_grid(di, li, ni; origin=origin) # nodes at the center and vertices of the cells
-    dt = Inf
+    ly           = 1e0          # domain length in y
+    lx           = ly           # domain length in x
+    ni           = nx, ny       # number of cells
+    li           = lx, ly       # domain length in x- and y-
+    di           = @. li / ni   # grid step in x- and -y
+    origin       = 0.0, 0.0     # origin coordinates
+    grid         = Geometry(ni, li; origin = origin)
+    (; xci, xvi) = grid # nodes at the center and vertices of the cells
+    dt           = Inf
 
     # Physical properties using GeoParams ----------------
-    η0 = 1e22           # viscosity
-    G0 = 10^10           # elastic shear modulus
-    εbg = 1e-14           # background strain-rate
-    dt = 1e11
-    el_bg = SetConstantElasticity(; G=G0, ν=0.5)
-    visc = LinearViscous(; η=η0)
+    η0       = 1e22           # viscosity
+    G0       = 10^10           # elastic shear modulus
+    εbg      = 1e-14           # background strain-rate
+    dt       = 1e11
+    el_bg    = SetConstantElasticity(; G=G0, ν=0.5)
+    visc     = LinearViscous(; η=η0)
     rheology = (
         # Low density phase
         SetMaterialParams(;
@@ -57,22 +58,22 @@ function main(igg; nx=64, ny=64, figdir="model_figs")
     )
 
     # Initialize phase ratios -------------------------------
-    radius = 0.1
+    radius       = 0.1
     phase_ratios = PhaseRatio(ni, length(rheology))
     init_phases!(phase_ratios, xci, radius)
 
     # STOKES ---------------------------------------------
     # Allocate arrays needed for every Stokes problem
-    stokes = StokesArrays(ni, ViscoElastic)
+    stokes    = StokesArrays(ni, ViscoElastic)
     pt_stokes = PTStokesCoeffs(li, di; ϵ=1e-6, CFL=0.75 / √2.1)
 
     # Buoyancy forces
-    ρg = @zeros(ni...), @zeros(ni...)
+    ρg     = @zeros(ni...), @zeros(ni...)
     ρg[2] .= rheology[1].Density[1].ρ.val .* rheology[1].Gravity[1].g.val
-    args = (; T=@zeros(ni...), P=stokes.P, dt=dt)
+    args   = (; T=@zeros(ni...), P=stokes.P, dt=dt)
 
     # Rheology
-    η = @ones(ni...)
+    η     = @ones(ni...)
     η_vep = similar(η) # effective visco-elasto-plastic viscosity
     @parallel (@idx ni) compute_viscosity!(
         η,
@@ -94,18 +95,19 @@ function main(igg; nx=64, ny=64, figdir="model_figs")
     stokes.V.Vx .= PTArray([x * εbg for x in xvi[1], _ in 1:(ny + 2)])
     stokes.V.Vy .= PTArray([-y * εbg for _ in 1:(nx + 2), y in xvi[2]])
     flow_bcs!(stokes, flow_bcs) # apply boundary conditions
+    update_halo!(stokes.V.Vx, stokes.V.Vy)
     # IO ------------------------------------------------
     # if it does not exist, make folder where figures are stored
     !isdir(figdir) && mkpath(figdir)
     # ----------------------------------------------------
 
     # Time loop
     t, it = 0.0, 0
-    tmax = 1.0e13
-    τII = Float64[0.0]
-    sol = Float64[0.0]
-    ttot = Float64[0.0]
-    P = Float64[0.0]
+    tmax  = 1.0e13
+    τII   = Float64[0.0]
+    sol   = Float64[0.0]
+    ttot  = Float64[0.0]
+    P     = Float64[0.0]
 
     while t < tmax
 
@@ -163,8 +165,8 @@ function main(igg; nx=64, ny=64, figdir="model_figs")
     return nothing
 end
 
-N = 32
-n = N + 2
+N  = 32
+n  = N + 2
 nx = n - 2
 ny = n - 2
 figdir = "ElasticBuildUp_incompressible"

miniapps/benchmarks/stokes2D/shear_band/ShearBand2D.jl

@@ -34,14 +34,15 @@ end
 function main(igg; nx=64, ny=64, figdir="model_figs")
 
     # Physical domain ------------------------------------
-    ly       = 1e0          # domain length in y
-    lx       = ly           # domain length in x
-    ni       = nx, ny       # number of cells
-    li       = lx, ly       # domain length in x- and y-
-    di       = @. li / ni   # grid step in x- and -y
-    origin   = 0.0, 0.0     # origin coordinates
-    xci, xvi = lazy_grid(di, li, ni; origin=origin) # nodes at the center and vertices of the cells
-    dt       = Inf
+    ly           = 1e0          # domain length in y
+    lx           = ly           # domain length in x
+    ni           = nx, ny       # number of cells
+    li           = lx, ly       # domain length in x- and y-
+    di           = @. li / ni   # grid step in x- and -y
+    origin       = 0.0, 0.0     # origin coordinates
+    grid         = Geometry(ni, li; origin = origin)
+    (; xci, xvi) = grid # nodes at the center and vertices of the cells
+    dt           = Inf
 
     # Physical properties using GeoParams ----------------
     τ_y     = 1.6           # yield stress. If do_DP=true, τ_y stand for the cohesion: c*cos(ϕ)
@@ -110,6 +111,7 @@ function main(igg; nx=64, ny=64, figdir="model_figs")
     stokes.V.Vx .= PTArray([ x*εbg for x in xvi[1], _ in 1:ny+2])
     stokes.V.Vy .= PTArray([-y*εbg for _ in 1:nx+2, y in xvi[2]])
     flow_bcs!(stokes, flow_bcs) # apply boundary conditions
+    update_halo!(stokes.V.Vx, stokes.V.Vy)
 
     # IO ------------------------------------------------
     # if it does not exist, make folder where figures are stored