first implementation for 2D with parallelstencil, not working

Iddingsite · Sep 25, 2023 · 84e396d · 84e396d
1 parent 859fbc3
commit 84e396d
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diff --git a/LocalPreferences.toml b/LocalPreferences.toml
@@ -0,0 +1,2 @@
+[DiffusionGarnet]
+backend = "Threads_Float64_2D"
diff --git a/Manifest.toml b/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -5,16 +5,20 @@ version = "1.0.0-DEV"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+ParallelStencil = "94395366-693c-11ea-3b26-d9b7aac5d958"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TerminalLoggers = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"

diff --git a/examples/2D/Contour_HR.txt b/examples/2D/Contour_HR.txt
diff --git a/examples/2D/Contour_LR.txt b/examples/2D/Contour_LR.txt
diff --git a/examples/2D/Xalm.txt b/examples/2D/Xalm.txt
diff --git a/examples/2D/Xalm_LR.txt b/examples/2D/Xalm_LR.txt
diff --git a/examples/2D/Xgrs.txt b/examples/2D/Xgrs.txt
diff --git a/examples/2D/Xgrs_LR.txt b/examples/2D/Xgrs_LR.txt
diff --git a/examples/2D/Xprp.txt b/examples/2D/Xprp.txt
diff --git a/examples/2D/Xprp_LR.txt b/examples/2D/Xprp_LR.txt
diff --git a/examples/2D/Xsps.txt b/examples/2D/Xsps.txt
diff --git a/examples/2D/Xsps_LR.txt b/examples/2D/Xsps_LR.txt
diff --git a/examples/2D/position_Grt.txt b/examples/2D/position_Grt.txt
diff --git a/examples/2D/position_Grt_LR.txt b/examples/2D/position_Grt_LR.txt
diff --git a/examples/Spherical/Grt_Spherical+1D.gif b/examples/Spherical/Grt_Spherical+1D.gif
diff --git a/src/DiffusionGarnet.jl b/src/DiffusionGarnet.jl
@@ -3,32 +3,68 @@ module DiffusionGarnet
 using Reexport
 
 @reexport using Plots
-@reexport using OrdinaryDiffEq
 @reexport using BenchmarkTools
-@reexport using Symbolics
 @reexport using Parameters
 @reexport using Unitful
 @reexport using DelimitedFiles
-@reexport using LinearAlgebra
 @reexport using DiffEqCallbacks
-# @reexport using ParallelStencil
 @reexport using Logging: global_logger
 @reexport using TerminalLoggers: TerminalLogger
+@reexport using ParallelStencil
+
+using OrdinaryDiffEq
+using Symbolics
+using ParallelStencil
+using Preferences
+
+
+
+# initialise ParallelStencil (Thx AlbertDeMontserrat!)
+function set_backend(new_backend::String)
+    if !(
+        new_backend ∈
+        ("Threads_Float64_2D", "Threads_Float32_2D", "CUDA_Float64_2D", "CUDA_Float32_2D",        "Threads_Float64_3D", "Threads_Float32_3D", "CUDA_Float64_3D", "CUDA_Float32_3D")
+    )
+        throw(ArgumentError("Invalid backend: \"$(new_backend)\""))
+    end
+
+    # Set it in our runtime values, as well as saving it to disk
+    @set_preferences!("backend" => new_backend)
+    @info("New backend set; restart your Julia session for this change to take effect!")
+end
+
+const backend = @load_preference("backend", "Threads_Float64_2D")
+
+export backend, set_backend
 
 function __init__()
     # initialise global logger for OrdinaryDiffEq
     global_logger(TerminalLogger())
+
+    # @require ParallelStencil = "94395366-693c-11ea-3b26-d9b7aac5d958" include("Discretisation/2D/semi_discretisation_2D.jl")
+end
+
+
+let
+    s = split(backend, "_")
+    device = s[1]
+    precision = s[2]
+    dimension = parse(Int, s[3][1])
+    @eval begin
+        @init_parallel_stencil($(Symbol(device)), $(Symbol(precision)), $dimension)
+    end
 end
 
 include("input/initialconditions.jl")
 include("callbacks/update_diffusion_coef_TP.jl")
 include("Discretisation/1D/semi_discretisation_1D.jl")
+include("Discretisation/2D/semi_discretisation_2D.jl")
 include("Discretisation/Spherical/semi_discretisation_spherical.jl")
 include("simulate/simulate.jl")
 
 export InitialConditions1D, InitialConditions2D, InitialConditions3D, InitialConditionsSpherical
 export D_ini!, Domain
-export semi_discretisation_diffusion_1D, semi_discretisation_diffusion_spherical
+export semi_discretisation_diffusion_1D, semi_discretisation_diffusion_spherical, semi_discretisation_diffusion_2D, Diffusion_coef_2D!, stencil_diffusion_2D!
 export simulate
 export update_diffusion_coef
 

diff --git a/src/Discretisation/2D/semi_discretisation_2D.jl b/src/Discretisation/2D/semi_discretisation_2D.jl
@@ -0,0 +1,164 @@
+
+import Base.@propagate_inbounds
+
+@parallel_indices (iy, ix) function Diffusion_coef_2D!(DMgMg, DMgFe, DMgMn, DFeMg, DFeFe, DFeMn, DMnMg, DMnFe, DMnMn, CMg, CFe ,CMn, D0, D_charact, grt_position)
+
+    @propagate_inbounds @inline sum_D(CMg, CFe, CMn, D0, ix, iy) = D0[1] * CMg[iy, ix] + D0[2] * CFe[iy, ix] + D0[3] * CMn[iy, ix] +
+        D0[4] * (1 - CMg[iy, ix] - CFe[iy, ix] - CMn[iy, ix])
+
+    if ix>1 && ix<size(DMgMg,2) && iy>1 && iy<size(DMgMg,1)
+        if grt_position[iy,ix] == 1.0
+            DMgMg[iy,ix] = (D0[1] - D0[1] * CMg[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[1] - D0[end])) / D_charact
+            DMgFe[iy,ix] = (      - D0[1] * CMg[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[2] - D0[end])) / D_charact
+            DMgMn[iy,ix] = (      - D0[1] * CMg[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[3] - D0[end])) / D_charact
+            DFeMg[iy,ix] = (      - D0[2] * CFe[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[1] - D0[end])) / D_charact
+            DFeFe[iy,ix] = (D0[2] - D0[2] * CFe[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[2] - D0[end])) / D_charact
+            DFeMn[iy,ix] = (      - D0[2] * CFe[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[3] - D0[end])) / D_charact
+            DMnMg[iy,ix] = (      - D0[3] * CMn[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[1] - D0[end])) / D_charact
+            DMnFe[iy,ix] = (      - D0[3] * CMn[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[2] - D0[end])) / D_charact
+            DMnMn[iy,ix] = (D0[3] - D0[3] * CMn[iy,ix] / sum_D(CMg,CFe,CMn,D0,ix,iy) * (D0[3] - D0[end])) / D_charact
+        else
+            DMgMg[iy,ix] = 0.0
+            DMgFe[iy,ix] = 0.0
+            DMgMn[iy,ix] = 0.0
+            DFeMg[iy,ix] = 0.0
+            DFeFe[iy,ix] = 0.0
+            DFeMn[iy,ix] = 0.0
+            DMnMg[iy,ix] = 0.0
+            DMnFe[iy,ix] = 0.0
+            DMnMn[iy,ix] = 0.0
+        end
+    end
+
+    return
+end
+
+
+@parallel_indices (iy, ix) function stencil_diffusion_2D!(dtCMg, dtCFe, dtCMn, CMg, CFe ,CMn, DMgMg, DMgFe, DMgMn, DFeMg, DFeFe, DFeMn, DMnMg, DMnFe, DMnMn, position_Grt, Grt_boundaries, Δxad_, Δyad_)
+
+    @propagate_inbounds @inline av_D_x(D, ix, iy) = 0.5 * (D[iy,ix] + D[iy,ix+1])
+    @propagate_inbounds @inline av_D_y(D, ix, iy) = 0.5 * (D[iy,ix] + D[iy+1,ix])
+    @propagate_inbounds @inline qx(D, C, ix, iy, Δxad_) = av_D_x(D, ix, iy) * (C[iy,ix+1]-C[iy,ix]) * Δxad_
+    @propagate_inbounds @inline qy(D, C, ix, iy, Δyad_) = av_D_y(D, ix, iy) * (C[iy+1,ix]-C[iy,ix]) * Δyad_
+
+
+    # iterate inside the arrays
+    if ix>1 && ix<size(dtCMg,2) && iy>1 && iy<size(dtCMg,1)
+        if position_Grt[iy,ix] == 1.0
+            dtCMg[iy,ix] = (qx(DMgMg,CMg,ix,iy,Δxad_) - qx(DMgMg,CMg,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DMgFe,CFe,ix,iy,Δxad_) - qx(DMgFe,CFe,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DMgMn,CMn,ix,iy,Δxad_) - qx(DMgMn,CMn,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qy(DMgMg,CMg,ix,iy,Δyad_) - qy(DMgMg,CMg,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DMgFe,CFe,ix,iy,Δyad_) - qy(DMgFe,CFe,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DMgMn,CMn,ix,iy,Δyad_) - qy(DMgMn,CMn,ix,iy-1,Δyad_)) * Δyad_
+            dtCFe[iy,ix] = (qx(DFeMg,CMg,ix,iy,Δxad_) - qx(DFeMg,CMg,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DFeFe,CFe,ix,iy,Δxad_) - qx(DFeFe,CFe,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DFeMn,CMn,ix,iy,Δxad_) - qx(DFeMn,CMn,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qy(DFeMg,CMg,ix,iy,Δyad_) - qy(DFeMg,CMg,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DFeFe,CFe,ix,iy,Δyad_) - qy(DFeFe,CFe,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DFeMn,CMn,ix,iy,Δyad_) - qy(DFeMn,CMn,ix,iy-1,Δyad_)) * Δyad_
+            dtCMn[iy,ix] = (qx(DMnMg,CMg,ix,iy,Δxad_) - qx(DMnMg,CMg,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DMnFe,CFe,ix,iy,Δxad_) - qx(DMnFe,CFe,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qx(DMnMn,CMn,ix,iy,Δxad_) - qx(DMnMn,CMn,ix-1,iy,Δxad_)) * Δxad_ +
+                           (qy(DMnMg,CMg,ix,iy,Δyad_) - qy(DMnMg,CMg,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DMnFe,CFe,ix,iy,Δyad_) - qy(DMnFe,CFe,ix,iy-1,Δyad_)) * Δyad_ +
+                           (qy(DMnMn,CMn,ix,iy,Δyad_) - qy(DMnMn,CMn,ix,iy-1,Δyad_)) * Δyad_
+            # first order Neumann if inclusions
+            # left
+            if position_Grt[iy,ix-1] == 0.0
+                dtCMg[iy,ix] -= - qx(DMgMg,CMg,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DMgFe,CFe,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DMgMn,CMn,ix-1,iy,Δxad_) * Δxad_
+                dtCFe[iy,ix] -= - qx(DFeMg,CMg,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DFeFe,CFe,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DFeMn,CMn,ix-1,iy,Δxad_) * Δxad_
+                dtCMn[iy,ix] -= - qx(DMnMg,CMg,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DMnFe,CFe,ix-1,iy,Δxad_) * Δxad_ -
+                                  qx(DMnMn,CMn,ix-1,iy,Δxad_) * Δxad_
+            end
+            # right
+            if position_Grt[iy,ix+1] == 0.0
+                dtCMg[iy,ix] -= qx(DMgMg,CMg,ix,iy,Δxad_) * Δxad_ +
+                                qx(DMgFe,CFe,ix,iy,Δxad_) * Δxad_ +
+                                qx(DMgMn,CMn,ix,iy,Δxad_) * Δxad_
+                dtCFe[iy,ix] -= qx(DFeMg,CMg,ix,iy,Δxad_) * Δxad_ +
+                                qx(DFeFe,CFe,ix,iy,Δxad_) * Δxad_ +
+                                qx(DFeMn,CMn,ix,iy,Δxad_) * Δxad_
+                dtCMn[iy,ix] -= qx(DMnMg,CMg,ix,iy,Δxad_) * Δxad_ +
+                                qx(DMnFe,CFe,ix,iy,Δxad_) * Δxad_ +
+                                qx(DMnMn,CMn,ix,iy,Δxad_) * Δxad_
+            end
+            # bottom
+            if position_Grt[iy-1,ix] == 0.0
+                dtCMg[iy,ix] -= - qy(DMgMg,CMg,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DMgFe,CFe,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DMgMn,CMn,ix,iy-1,Δyad_) * Δyad_
+                dtCFe[iy,ix] -= - qy(DFeMg,CMg,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DFeFe,CFe,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DFeMn,CMn,ix,iy-1,Δyad_) * Δyad_
+                dtCMn[iy,ix] -= - qy(DMnMg,CMg,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DMnFe,CFe,ix,iy-1,Δyad_) * Δyad_ -
+                                  qy(DMnMn,CMn,ix,iy-1,Δyad_) * Δyad_
+            end
+            # top
+            if position_Grt[iy+1,ix] == 0.0
+                dtCMg[iy,ix] -= qy(DMgMg,CMg,ix,iy,Δyad_) * Δyad_ +
+                                qy(DMgFe,CFe,ix,iy,Δyad_) * Δyad_ +
+                                qy(DMgMn,CMn,ix,iy,Δyad_) * Δyad_
+                dtCFe[iy,ix] -= qy(DFeMg,CMg,ix,iy,Δyad_) * Δyad_ +
+                                qy(DFeFe,CFe,ix,iy,Δyad_) * Δyad_ +
+                                qy(DFeMn,CMn,ix,iy,Δyad_) * Δyad_
+                dtCMn[iy,ix] -= qy(DMnMg,CMg,ix,iy,Δyad_) * Δyad_ +
+                                qy(DMnFe,CFe,ix,iy,Δyad_) * Δyad_ +
+                                qy(DMnMn,CMn,ix,iy,Δyad_) * Δyad_
+            end
+        # if point is an inclusion
+        else
+            dtCMg[iy,ix] = 0.0
+            dtCFe[iy,ix] = 0.0
+            dtCMn[iy,ix] = 0.0
+        end
+        # if point is on grain boundary
+        if Grt_boundaries[iy,ix] == 1.0
+            dtCMg[iy,ix] = 0.0
+            dtCFe[iy,ix] = 0.0
+            dtCMn[iy,ix] = 0.0
+        end
+    # if point is on a model boundary (can define Neumann here)
+    else
+        dtCMg[iy,ix] = 0.0
+        dtCFe[iy,ix] = 0.0
+        dtCMn[iy,ix] = 0.0
+    end
+
+    return
+end
+
+
+function semi_discretisation_diffusion_2D(du,u,p,t)
+
+    @unpack D, D0, D_charact, Δxad_, Δyad_ = p
+    @unpack grt_position, grt_boundary = p.IC
+    DMgMg, DMgFe, DMgMn, DFeMg, DFeFe, DFeMn, DMnMg, DMnFe, DMnMn = D
+
+    CMg = @view u[:,:,1]
+    CFe = @view u[:,:,2]
+    CMn = @view u[:,:,3]
+
+    dtCMg = @view du[:,:,1]
+    dtCFe = @view du[:,:,2]
+    dtCMn = @view du[:,:,3]
+
+    println(typeof(du))
+
+    # update diffusive parameters
+    @parallel Diffusion_coef_2D!(DMgMg, DMgFe, DMgMn, DFeMg, DFeFe, DFeMn, DMnMg, DMnFe, DMnMn,
+                                 CMg, CFe ,CMn, D0, D_charact, grt_position)
+
+
+    # semi-discretization
+    @parallel stencil_diffusion_2D!(dtCMg, dtCFe, dtCMn, CMg, CFe ,CMn,
+                                 DMgMg, DMgFe, DMgMn, DFeMg, DFeFe, DFeMn, DMnMg, DMnFe, DMnMn,
+                                 grt_position, grt_boundary, Δxad_, Δyad_)
+end
+