Merge pull request #13 from slimgroup/rename

Rename
slimgroup · Mar 10, 2023 · a94e085 · mloubout · Mar 16, 2023 · a94e085
2 parents 947483c + d64341b
commit a94e085
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diff --git a/.github/workflows/ci-runtest.yml b/.github/workflows/ci-runtest.yml
@@ -1,4 +1,4 @@
-name: CI-JutulDarcyAD
+name: CI-JutulDarcyRules
 
 on: 
   # Trigger the workflow on push to main or pull request
@@ -29,7 +29,7 @@ jobs:
           - x64
 
     steps:
-      - name: Checkout JutulDarcyAD
+      - name: Checkout JutulDarcyRules
         uses: actions/checkout@v2
 
       - name: Setup julia

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
-name = "JutulDarcyAD"
+name = "JutulDarcyRules"
 uuid = "41f0c4f5-9bdd-4ef1-8c3a-d454dff2d562"
 authors = ["Ziyi Yin <[email protected]>"]
-version = "0.2.1"
+version = "0.2.2"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-<h1 align="center">JutulDarcyAD: auto-differentiable two-phase flow solvers based on Jutul and JutulDarcy</h1>
+<h1 align="center">JutulDarcyRules: auto-differentiable two-phase flow solvers based on Jutul and JutulDarcy</h1>
 
 [![][license-img]][license-status] [![][zenodo-img]][zenodo-status]
 
@@ -22,5 +22,5 @@ SLIM public GitHub account, [https://github.com/slimgroup](https://github.com/sl
 [ChainRules.jl]:https://github.com/JuliaDiff/ChainRules.jl
 [license-status]:LICENSE
 [license-img]:http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat?style=plastic
-[zenodo-status]:https://doi.org/10.5281/zenodo.7587717
-[zenodo-img]:https://zenodo.org/badge/DOI/10.5281/zenodo.7587717.svg?style=plastic
+[zenodo-status]:https://zenodo.org/badge/latestdoi/594128866
+[zenodo-img]:https://zenodo.org/badge/594128866.svg?style=plastic
diff --git a/examples/Project.toml b/examples/Project.toml
@@ -1,4 +1,4 @@
-name = "JutulDarcyAD-example"
+name = "JutulDarcyRules-example"
 authors = ["Ziyi Yin"]
 
 [deps]

diff --git a/examples/Vwell_2D.jl b/examples/Vwell_2D.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for fluid-flow simulation
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 
@@ -52,6 +52,6 @@ subplot(1,2,2);
 imshow(reshape(Pressure(states0.states[end]), n[1], n[end])'); colorbar(); title("pressure")
 
 exist_co2 = sum(Saturations(states.states[end]) .* states.states[end].state[:Reservoir][:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-inj_co2 = JutulDarcyAD.ρCO2 * q.irate * JutulDarcyAD.day * sum(tstep)
+inj_co2 = JutulDarcyRules.ρCO2 * q.irate * JutulDarcyRules.day * sum(tstep)
 
 norm(exist_co2-inj_co2)/norm(exist_co2+inj_co2)
diff --git a/examples/basic2D.jl b/examples/basic2D.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for fluid-flow simulation
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 
@@ -52,6 +52,6 @@ subplot(1,2,2);
 imshow(reshape(Pressure(states0.states[end]), n[1], n[end])'); colorbar(); title("pressure")
 
 exist_co2 = sum(Saturations(states.states[end]) .* states.states[end].state[:Reservoir][:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-inj_co2 = JutulDarcyAD.ρCO2 * q.irate * JutulDarcyAD.day * sum(tstep)
+inj_co2 = JutulDarcyRules.ρCO2 * q.irate * JutulDarcyRules.day * sum(tstep)
 
 norm(exist_co2-inj_co2)/norm(exist_co2+inj_co2)
diff --git a/examples/compass.jl b/examples/compass.jl
@@ -1,9 +1,9 @@
 ## A 2D compass example
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/end2end.jl b/examples/end2end.jl
@@ -1,9 +1,9 @@
 ## A 64×64 2D example for end-to-end inversion of a tortuous channel
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/inv_2D.jl b/examples/inv_2D.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for permeability inversion
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/inv_logK.jl b/examples/inv_logK.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for permeability inversion
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/inv_tortuous.jl b/examples/inv_tortuous.jl
@@ -1,9 +1,9 @@
 ## A 64×64 2D example for permeability inversion of a tortuous channel
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/inv_trans.jl b/examples/inv_trans.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for transmissibility inversion
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 using Flux

diff --git a/examples/optim_K.jl b/examples/optim_K.jl
@@ -1,7 +1,7 @@
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using Flux
 using LinearAlgebra
 using Optim

diff --git a/examples/simple_2D.jl b/examples/simple_2D.jl
@@ -1,9 +1,9 @@
 ## A simple 2D example for fluid-flow simulation
 
 using DrWatson
-@quickactivate "JutulDarcyAD-example"
+@quickactivate "JutulDarcyRules-example"
 
-using JutulDarcyAD
+using JutulDarcyRules
 using LinearAlgebra
 using PyPlot
 

diff --git a/src/FlowAD/FlowAD.jl → src/FlowRules/FlowRules.jl b/src/FlowAD/FlowAD.jl → src/FlowRules/FlowRules.jl
diff --git a/src/FlowAD/Operators/jutulModeling.jl → src/FlowRules/Operators/jutulModeling.jl b/src/FlowAD/Operators/jutulModeling.jl → src/FlowRules/Operators/jutulModeling.jl
diff --git a/src/FlowAD/Operators/rrule.jl → src/FlowRules/Operators/rrule.jl b/src/FlowAD/Operators/rrule.jl → src/FlowRules/Operators/rrule.jl
diff --git a/src/FlowAD/Types/jutulForce.jl → src/FlowRules/Types/jutulForce.jl b/src/FlowAD/Types/jutulForce.jl → src/FlowRules/Types/jutulForce.jl
diff --git a/src/FlowAD/Types/jutulModel.jl → src/FlowRules/Types/jutulModel.jl b/src/FlowAD/Types/jutulModel.jl → src/FlowRules/Types/jutulModel.jl
diff --git a/src/FlowAD/Types/jutulSource.jl → src/FlowRules/Types/jutulSource.jl b/src/FlowAD/Types/jutulSource.jl → src/FlowRules/Types/jutulSource.jl
diff --git a/src/FlowAD/Types/jutulState.jl → src/FlowRules/Types/jutulState.jl b/src/FlowAD/Types/jutulState.jl → src/FlowRules/Types/jutulState.jl
diff --git a/src/FlowAD/Types/jutulVWell.jl → src/FlowRules/Types/jutulVWell.jl b/src/FlowAD/Types/jutulVWell.jl → src/FlowRules/Types/jutulVWell.jl
diff --git a/src/FlowAD/Types/type_utils.jl → src/FlowRules/Types/type_utils.jl b/src/FlowAD/Types/type_utils.jl → src/FlowRules/Types/type_utils.jl
diff --git a/src/JutulDarcyAD.jl → src/JutulDarcyRules.jl b/src/JutulDarcyAD.jl → src/JutulDarcyRules.jl
@@ -1,7 +1,7 @@
 __precompile__()
-module JutulDarcyAD
+module JutulDarcyRules
 
-    export JutulDarcyADPATH, Darcy, md
+    export JutulDarcyRulesPATH, Darcy, md
 
     using LinearAlgebra
     using Statistics
@@ -19,7 +19,7 @@ module JutulDarcyAD
     import LinearAlgebra: norm, dot
     import ChainRulesCore: rrule
 
-    JutulDarcyADPATH = dirname(pathof(JutulDarcyAD))
+    JutulDarcyRulesPATH = dirname(pathof(JutulDarcyRules))
 
     visCO2 = 1e-4
     visH2O = 1e-3
@@ -33,6 +33,6 @@ module JutulDarcyAD
     const day = 24*3600.0
 
     include("PropertyConversion/PropertyConversion.jl")
-    include("FlowAD/FlowAD.jl")
+    include("FlowRules/FlowRules.jl")
 
-end # module JutulDarcyAD
+end # module JutulDarcyRules
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,6 +1,6 @@
 using Test
 using Jutul
-using JutulDarcyAD
+using JutulDarcyRules
 using Flux
 using Printf
 using Random

diff --git a/test/test_jutulModeling.jl b/test/test_jutulModeling.jl
@@ -11,7 +11,7 @@ x0 = log.(KtoTrans(CartesianMesh(model0), model0.K))
     states = S(x, q)
     for i = 1:length(states.states)
         exist_co2 = sum(Saturations(states.states[i]) .* states.states[i].state[:Reservoir][:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-        inj_co2 = JutulDarcyAD.ρCO2 * q.irate * JutulDarcyAD.day * sum(tstep[1:i])
+        inj_co2 = JutulDarcyRules.ρCO2 * q.irate * JutulDarcyRules.day * sum(tstep[1:i])
         @test isapprox(exist_co2, inj_co2) rtol=1e-3
     end
 end
@@ -20,7 +20,7 @@ end
     states = S(x, q1)
     for i = 1:length(states.states)
         exist_co2 = sum(Saturations(states.states[i]) .* states.states[i].state[:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-        inj_co2 = JutulDarcyAD.ρCO2 * q.irate * JutulDarcyAD.day * sum(S.tstep[1:i])
+        inj_co2 = JutulDarcyRules.ρCO2 * q.irate * JutulDarcyRules.day * sum(S.tstep[1:i])
         @test isapprox(exist_co2, inj_co2) rtol=1e-3
     end
 end
@@ -33,7 +33,7 @@ end
     states_end = S(x, q2; state0=states)
     for i = 1:length(states_end.states)
         exist_co2 = sum(Saturations(states_end.states[i]) .* states_end.states[i].state[:Reservoir][:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-        inj_co2 = JutulDarcyAD.ρCO2 * q2.irate * JutulDarcyAD.day * sum(S.tstep[1:i])
+        inj_co2 = JutulDarcyRules.ρCO2 * q2.irate * JutulDarcyRules.day * sum(S.tstep[1:i])
         @test isapprox(exist_co2-pre_co2, inj_co2) rtol=1e-3
     end
 end
@@ -42,7 +42,7 @@ end
     states = S(x, q2)
     for i = 1:length(states.states)
         exist_co2 = sum(Saturations(states.states[i]) .* states.states[i].state[:Reservoir][:PhaseMassDensities][1,:] .* model.ϕ) * prod(model.d)
-        inj_co2 = JutulDarcyAD.ρCO2 * q.irate * JutulDarcyAD.day * sum(tstep[1:i])
+        inj_co2 = JutulDarcyRules.ρCO2 * q.irate * JutulDarcyRules.day * sum(tstep[1:i])
         @test isapprox(exist_co2, inj_co2) rtol=1e-3
     end
 end
diff --git a/test/test_jutulState.jl b/test/test_jutulState.jl
@@ -24,6 +24,6 @@ model, model0, q, q1, q2, init_state, init_state_simple, tstep = test_config();
 
     @info "test translation"
     half_init_state = init_state(vec(init_state) ./ 2)
-    JutulDarcyAD.check_valid_state(half_init_state)
+    JutulDarcyRules.check_valid_state(half_init_state)
     @test vec(half_init_state) == 0.5 * vec(init_state)
 end
diff --git a/test/test_utils.jl b/test/test_utils.jl
@@ -21,7 +21,7 @@ function test_config()
     q = jutulForce(irate, inj_loc)
     q1 = jutulSource(irate, [inj_loc, prod_loc])
     q2 = jutulVWell(irate, inj_loc[1:2]; startz = 9 * d[3], endz = 11 * d[3])
-    state0 = jutulState(JutulDarcyAD.setup_well_model(model, q, tstep)[3])
+    state0 = jutulState(JutulDarcyRules.setup_well_model(model, q, tstep)[3])
     state1 = jutulSimpleState(model)
     return model, model0, q, q1, q2, state0, state1, tstep
 end