Merge branch 'main' into pa-restart

PTsolvers · May 7, 2024 · 7547dd2 · 7547dd2
2 parents ecb54e7 + 5a30156
commit 7547dd2
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diff --git a/Project.toml b/Project.toml
@@ -33,7 +33,7 @@ AMDGPU = "0.6, 0.7, 0.8"
 Adapt = "3"
 CUDA = "4.4.1, 5"
 CellArrays = "0.2"
-GeoParams = "0.5"
+GeoParams = "0.5.8"
 HDF5 = "0.17.1"
 ImplicitGlobalGrid = "0.15.0"
 MPI = "0.20"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,6 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-GeoParams = "e018b62d-d9de-4a26-8697-af89c310ae38"
 JustRelax = "34418575-392d-4e26-8c6d-96b0910afa06"
 
 [compat]

diff --git a/docs/make.jl b/docs/make.jl
@@ -11,7 +11,7 @@ makedocs(;
 
     warnonly = Documenter.except(:footnote),
     pages=[
-        "Home"      => "man/index.md",
+        "Home"      => "index.md",
         "User guide"=> Any[
             "Installation" => "man/installation.md",
             "Backend"   => "man/backend.md",

diff --git a/docs/src/assets/Blankenbach_Temp.png b/docs/src/assets/Blankenbach_Temp.png
diff --git a/docs/src/assets/Blankenbach_Time_Series_V_Nu.png b/docs/src/assets/Blankenbach_Time_Series_V_Nu.png
diff --git a/docs/src/man/index.md → docs/src/index.md b/docs/src/man/index.md → docs/src/index.md
@@ -18,7 +18,7 @@ The package serves several purposes:
   * It provides a collection of solvers to be used in quickly developing new applications
   * It provides some standardization so that application codes can
 
-     - more easily handle local material properties through the use of [GeoParams.jl]((https://github.com/JuliaGeodynamics/GeoParams.jl))
+     - more easily handle local material properties through the use of [GeoParams.jl](https://github.com/JuliaGeodynamics/GeoParams.jl)
      - more easily switch between a pseudo-transient solver and another solvers (e.g. an explicit thermal solvers)
 
   * It provides a natural repository for contributions of new solvers for use by the larger community

diff --git a/docs/src/man/Blankenbach.md b/docs/src/man/Blankenbach.md
@@ -392,7 +392,7 @@ fig
 
 ### Final model
 Temperature field
-![Temperatuere](../assets/Blankenbach/Temp.png)
+![Temperature](../assets/Blankenbach_Temp.png)
 
 And time history of the rms-velocity and Nusselt number
-![time series](../assets/Blankenbach/Time_Series_V_Nu.png)
+![time series](../assets/Blankenbach_Time_Series_V_Nu.png)
diff --git a/docs/src/man/listfunctions.md b/docs/src/man/listfunctions.md
@@ -2,5 +2,5 @@
 
 Here an overview of all functions:
 ```@autodocs
-Modules = [JustRelax]
+Modules = [JustRelax, JustRelax.JustRelax2D, JustRelax.JustRelax3D, JustRelax.DataIO]
 ```
diff --git a/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_WENO5.jl b/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_WENO5.jl
@@ -85,7 +85,7 @@ function main2D(igg; ar=1, nx=32, ny=32, nit = 1e1, figdir="figs2D", do_vtk =fal
     pPhases,            = init_cell_arrays(particles, Val(1))
     phase_ratios        = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------

diff --git a/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_sgd.jl b/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_sgd.jl
@@ -86,7 +86,7 @@ function main2D(igg; ar=1, nx=32, ny=32, nit = 1e1, figdir="figs2D", do_vtk =fal
     particle_args       = (pT, pT0, pPhases)
     phase_ratios        = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -257,7 +257,7 @@ function main2D(igg; ar=1, nx=32, ny=32, nit = 1e1, figdir="figs2D", do_vtk =fal
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer, ), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         # Nusselt number, Nu = H/ΔT/L ∫ ∂T/∂z dx ----
         Nu_it   =   (ly / (1000.0*lx)) *

diff --git a/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_sgd_scaled.jl b/miniapps/benchmarks/stokes2D/Blankenbach2D/Benchmark2D_sgd_scaled.jl
@@ -78,7 +78,7 @@ function main2D(igg; ar=1, nx=32, ny=32, nit = 1e1, figdir="figs2D", do_vtk =fal
     particle_args       = (pT, pT0, pPhases)
     phase_ratios        = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -247,7 +247,7 @@ function main2D(igg; ar=1, nx=32, ny=32, nit = 1e1, figdir="figs2D", do_vtk =fal
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer, ), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         # Nusselt number, Nu = ∫ ∂T/∂z dx ----
         Nu_it   =   sum( ((abs.(thermal.T[2:end-1,end] - thermal.T[2:end-1,end-1])) ./ di[2]) .*di[1])

diff --git a/miniapps/benchmarks/stokes2D/VanKeken.jl/VanKeken.jl b/miniapps/benchmarks/stokes2D/VanKeken.jl/VanKeken.jl
@@ -86,7 +86,7 @@ function main2D(igg; ny=64, nx=64, figdir="model_figs")
     particle_args        = (pPhases, )
     phase_ratios         = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
     # STOKES ---------------------------------------------
     # Allocate arrays needed for every Stokes problem
@@ -170,7 +170,7 @@ function main2D(igg; ny=64, nx=64, figdir="model_figs")
         # inject && break
         inject_particles_phase!(particles, pPhases, (), (), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/benchmarks/stokes2D/free_surface_stabilization/PlumeFreeSurface_2D.jl b/miniapps/benchmarks/stokes2D/free_surface_stabilization/PlumeFreeSurface_2D.jl
@@ -120,7 +120,7 @@ function main(igg, nx, ny)
     # Elliptical temperature anomaly
     init_phases!(pPhases, particles)
     phase_ratios  = PhaseRatio(backend_JR, ni, length(rheology))
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -186,7 +186,7 @@ function main(igg, nx, ny)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (), (), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/benchmarks/stokes2D/free_surface_stabilization/RayleighTaylor2D.jl b/miniapps/benchmarks/stokes2D/free_surface_stabilization/RayleighTaylor2D.jl
@@ -118,7 +118,7 @@ function RT_2D(igg, nx, ny)
     A             = 5e3    # Amplitude of the anomaly
     phase_ratios  = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, A)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -197,7 +197,7 @@ function RT_2D(igg, nx, ny)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (), (), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/benchmarks/stokes2D/shear_heating/Shearheating2D.jl b/miniapps/benchmarks/stokes2D/shear_heating/Shearheating2D.jl
@@ -81,7 +81,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
     r_anomaly        = 3e3    # radius of perturbation
     phase_ratios     = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, xc_anomaly, yc_anomaly, r_anomaly)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -245,7 +245,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/benchmarks/stokes2D/sinking_block/SinkingBlock2D.jl b/miniapps/benchmarks/stokes2D/sinking_block/SinkingBlock2D.jl
@@ -115,7 +115,7 @@ function sinking_block2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", thermal_per
     r_anomaly    =  50e3   # radius of perturbation
     phase_ratios = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, xc_anomaly, abs(yc_anomaly), r_anomaly)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
     # STOKES ---------------------------------------------
     # Allocate arrays needed for every Stokes problem

diff --git a/miniapps/benchmarks/stokes3D/shear_heating/Shearheating3D.jl b/miniapps/benchmarks/stokes3D/shear_heating/Shearheating3D.jl
@@ -75,7 +75,7 @@ function main3D(igg; ar=8, ny=16, nx=ny*8, nz=ny*8, figdir="figs3D", do_vtk =fal
     r_anomaly        = 3e3    # radius of perturbation
     init_phases!(backend_JR, pPhases, particles, xc_anomaly, yc_anomaly, zc_anomaly, r_anomaly)
     phase_ratios     = PhaseRatio(ni, length(rheology))
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -227,7 +227,7 @@ function main3D(igg; ar=8, ny=16, nx=ny*8, nz=ny*8, figdir="figs3D", do_vtk =fal
             # check if we need to inject particles
             inject_particles_phase!(particles, pPhases, (pT, ), (thermal.T,), xvi)
             # update phase ratios
-            phase_ratios_center(phase_ratios, particles, grid, pPhases)
+            phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
             @show it += 1
             t        += dt

diff --git a/miniapps/benchmarks/thermal_diffusion/diffusion/diffusion2D_multiphase.jl b/miniapps/benchmarks/thermal_diffusion/diffusion/diffusion2D_multiphase.jl
@@ -126,7 +126,7 @@ function diffusion_2D(; nx=32, ny=32, lx=100e3, ly=100e3, Cp0=1.2e3, K0=3.0)
     pPhases,     = init_cell_arrays(particles, Val(1))
     phase_ratios = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, center_perturbation..., r)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     @parallel (@idx ni) compute_temperature_source_terms!(thermal.H, rheology, phase_ratios.center, args)

diff --git a/miniapps/benchmarks/thermal_diffusion/diffusion/diffusion3D_multiphase.jl b/miniapps/benchmarks/thermal_diffusion/diffusion/diffusion3D_multiphase.jl
@@ -145,7 +145,7 @@ function diffusion_3D(;
     pPhases,     = init_cell_arrays(particles, Val(1))
     phase_ratios = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, center_perturbation..., r)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # PT coefficients for thermal diffusion

diff --git a/miniapps/benchmarks/thermal_stress/Thermal_Stress_Magma_Chamber_nondim.jl b/miniapps/benchmarks/thermal_stress/Thermal_Stress_Magma_Chamber_nondim.jl
@@ -241,7 +241,7 @@ function main2D(igg; figdir=figdir, nx=nx, ny=ny, do_vtk=false)
     anomaly      = nondimensionalize((750 + 273)K, CharDim) # thermal perturbation (in K)
     init_phases!(pPhases, particles, x_anomaly, y_anomaly, r_anomaly, sticky_air, nondimensionalize(0.0km,CharDim), nondimensionalize(20km,CharDim))
     phase_ratios = PhaseRatio(backend_JR, ni, length(rheology))
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
     # Initialisation of thermal profile
     thermal     = ThermalArrays(backend_JR, ni) # initialise thermal arrays and boundary conditions
@@ -438,7 +438,7 @@ function main2D(igg; figdir=figdir, nx=nx, ny=ny, do_vtk=false)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         particle2grid!(T_buffer, pT, xvi, particles)
         @views T_buffer[:, end]        .= Tsurf

diff --git a/miniapps/benchmarks/thermal_stress/Thermal_Stress_Magma_Chamber_nondim3D.jl b/miniapps/benchmarks/thermal_stress/Thermal_Stress_Magma_Chamber_nondim3D.jl
@@ -242,7 +242,7 @@ function main3D(igg; figdir = "output", nx = 64, ny = 64, nz = 64, do_vtk = fals
     anomaly      = nondimensionalize((750 + 273)K, CharDim)               # thermal perturbation (in K)
     phase_ratios = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, x_anomaly, y_anomaly, z_anomaly, r_anomaly, sticky_air, nondimensionalize(0.0km,CharDim), nondimensionalize(20km,CharDim))
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
     # Initialisation of thermal profile
     thermal     = ThermalArrays(backend_JR, ni) # initialise thermal arrays and boundary conditions
@@ -420,7 +420,7 @@ function main3D(igg; figdir = "output", nx = 64, ny = 64, nz = 64, do_vtk = fals
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (thermal.T,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         particle2grid!(thermal.T, pT, xvi, particles)
         @views thermal.T[:, :, end] .= Tsurf

diff --git a/miniapps/convection/Particles2D/Layered_convection2D.jl b/miniapps/convection/Particles2D/Layered_convection2D.jl
@@ -128,7 +128,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
     r_anomaly        = 25e3    # radius of perturbation
     phase_ratios     = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, lx, yc_anomaly, r_anomaly, thick_air)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -292,7 +292,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/convection/Particles2D_nonDim/Layered_convection2D.jl b/miniapps/convection/Particles2D_nonDim/Layered_convection2D.jl
@@ -135,7 +135,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
     r_anomaly        = nondimensionalize(25km, CharDim) # radius of perturbation
     phase_ratios     = PhaseRatio(backend_JR, ni, length(rheology))
     init_phases!(pPhases, particles, lx, yc_anomaly, r_anomaly, thick_air, CharDim)
-    phase_ratios_center(phase_ratios, particles, grid, pPhases)
+    phase_ratios_center!(phase_ratios, particles, grid, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -298,7 +298,7 @@ function main2D(igg; ar=8, ny=16, nx=ny*8, figdir="figs2D", do_vtk =false)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt

diff --git a/miniapps/convection/Particles3D/Layered_convection3D.jl b/miniapps/convection/Particles3D/Layered_convection3D.jl
@@ -115,7 +115,7 @@ function main3D(igg; ar=1, nx=16, ny=16, nz=16, figdir="figs3D", do_vtk =false)
     r_anomaly        = 50e3   # radius of perturbation
     init_phases!(pPhases, particles, lx, ly; d=abs(zc_anomaly), r=r_anomaly)
     phase_ratios     = PhaseRatio(backend_JR, ni, length(rheology))
-    @parallel (@idx ni) phase_ratios_center(phase_ratios.center, particles.coords, xci, di, pPhases)
+    @parallel (@idx ni) phase_ratios_center!(phase_ratios.center, particles.coords, xci, di, pPhases)
     # ----------------------------------------------------
 
     # STOKES ---------------------------------------------
@@ -264,7 +264,7 @@ function main3D(igg; ar=1, nx=16, ny=16, nz=16, figdir="figs3D", do_vtk =false)
         # check if we need to inject particles
         inject_particles_phase!(particles, pPhases, (pT, ), (T_buffer,), xvi)
         # update phase ratios
-        phase_ratios_center(phase_ratios, particles, grid, pPhases)
+        phase_ratios_center!(phase_ratios, particles, grid, pPhases)
 
         @show it += 1
         t        += dt