From 0d38d3c6c96488a4acdefb7f58b7a231bd74d247 Mon Sep 17 00:00:00 2001
From: Santiago Badia <santiago.badia@monash.edu>
Date: Mon, 8 Nov 2021 08:04:57 +1100
Subject: [PATCH] some renaming and updated readme

---
 README.md                                         |  5 ++---
 test/TransientFEsTests/AffineFEOperatorsTests.jl  |  4 ++--
 .../BoundaryHeatEquationTests.jl                  |  4 ++--
 .../TransientFEsTests/ConstantFEOperatorsTests.jl |  4 ++--
 test/TransientFEsTests/DGHeatEquationTests.jl     |  4 ++--
 .../ForwardEulerHeatEquationTests.jl              |  4 ++--
 .../HeatEquationAutoDiffTests.jl                  |  4 ++--
 test/TransientFEsTests/HeatEquationTests.jl       |  4 ++--
 test/TransientFEsTests/HeatVectorEquationTests.jl |  8 ++++----
 .../StokesEquationAutoDiffTests.jl                |  4 ++--
 test/TransientFEsTests/StokesEquationTests.jl     |  4 ++--
 .../Transient2ndOrderFEOperatorsTests.jl          | 10 +++++-----
 .../TransientFEOperatorsTests.jl                  |  8 ++++----
 test/TransientFEsTests/TransientFETests.jl        | 15 +++++++--------
 test/TransientFEsTests/VectorHeatEquationTests.jl |  4 ++--
 15 files changed, 42 insertions(+), 44 deletions(-)

diff --git a/README.md b/README.md
index f94512e..942874f 100644
--- a/README.md
+++ b/README.md
@@ -62,9 +62,8 @@ U0 = U(0.0)
 uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
-solver = TransientFESolver(odes)
-sol_t = solve(solver,op,uh0,t0,tF)
+ode_solver = ThetaMethod(ls,dt,θ)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 for (uh_tn, tn) in sol_t
   # Here we have the solution uh_tn at tn
diff --git a/test/TransientFEsTests/AffineFEOperatorsTests.jl b/test/TransientFEsTests/AffineFEOperatorsTests.jl
index 3d36ad8..b68078b 100644
--- a/test/TransientFEsTests/AffineFEOperatorsTests.jl
+++ b/test/TransientFEsTests/AffineFEOperatorsTests.jl
@@ -54,8 +54,8 @@ U0 = U(0.0)
 uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
-sol_t = solve(odes,op,uh0,t0,tF)
+ode_solver = ThetaMethod(ls,dt,θ)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w*w
 
diff --git a/test/TransientFEsTests/BoundaryHeatEquationTests.jl b/test/TransientFEsTests/BoundaryHeatEquationTests.jl
index 70f5749..b5bdc0c 100644
--- a/test/TransientFEsTests/BoundaryHeatEquationTests.jl
+++ b/test/TransientFEsTests/BoundaryHeatEquationTests.jl
@@ -70,9 +70,9 @@ uh0 = interpolate_everywhere(u(0.0),U0)
 ls = LUSolver()
 using Gridap.Algebra: NewtonRaphsonSolver
 # nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 # Juno.@enter Base.iterate(sol_t)
 
diff --git a/test/TransientFEsTests/ConstantFEOperatorsTests.jl b/test/TransientFEsTests/ConstantFEOperatorsTests.jl
index 8ecaf4f..d1a852a 100644
--- a/test/TransientFEsTests/ConstantFEOperatorsTests.jl
+++ b/test/TransientFEsTests/ConstantFEOperatorsTests.jl
@@ -54,8 +54,8 @@ U0 = U(0.0)
 uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
-sol_t = solve(odes,op,uh0,t0,tF)
+ode_solver = ThetaMethod(ls,dt,θ)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w*w
 
diff --git a/test/TransientFEsTests/DGHeatEquationTests.jl b/test/TransientFEsTests/DGHeatEquationTests.jl
index 05eb2c5..05d0b65 100644
--- a/test/TransientFEsTests/DGHeatEquationTests.jl
+++ b/test/TransientFEsTests/DGHeatEquationTests.jl
@@ -69,9 +69,9 @@ uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
 using Gridap.Algebra: NewtonRaphsonSolver
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w*w
 
diff --git a/test/TransientFEsTests/ForwardEulerHeatEquationTests.jl b/test/TransientFEsTests/ForwardEulerHeatEquationTests.jl
index e82fb1a..2de154d 100644
--- a/test/TransientFEsTests/ForwardEulerHeatEquationTests.jl
+++ b/test/TransientFEsTests/ForwardEulerHeatEquationTests.jl
@@ -60,9 +60,9 @@ uh0 = interpolate_everywhere(u(0.0),U0)
 ls = LUSolver()
 using Gridap.Algebra: NewtonRaphsonSolver
 nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w*w
 
diff --git a/test/TransientFEsTests/HeatEquationAutoDiffTests.jl b/test/TransientFEsTests/HeatEquationAutoDiffTests.jl
index b4d5313..9fb494c 100644
--- a/test/TransientFEsTests/HeatEquationAutoDiffTests.jl
+++ b/test/TransientFEsTests/HeatEquationAutoDiffTests.jl
@@ -71,9 +71,9 @@ uh0 = interpolate_everywhere(u(0.0),U0)
 ls = LUSolver()
 using Gridap.Algebra: NewtonRaphsonSolver
 nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 # Juno.@enter Base.iterate(sol_t)
 
diff --git a/test/TransientFEsTests/HeatEquationTests.jl b/test/TransientFEsTests/HeatEquationTests.jl
index 992c08a..68d5319 100644
--- a/test/TransientFEsTests/HeatEquationTests.jl
+++ b/test/TransientFEsTests/HeatEquationTests.jl
@@ -56,9 +56,9 @@ uh0 = interpolate_everywhere(u(0.0),U0)
 ls = LUSolver()
 using Gridap.Algebra: NewtonRaphsonSolver
 nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 # Juno.@enter Base.iterate(sol_t)
 
diff --git a/test/TransientFEsTests/HeatVectorEquationTests.jl b/test/TransientFEsTests/HeatVectorEquationTests.jl
index 4262c34..58c213a 100644
--- a/test/TransientFEsTests/HeatVectorEquationTests.jl
+++ b/test/TransientFEsTests/HeatVectorEquationTests.jl
@@ -57,9 +57,9 @@ U0 = U(0.0)
 uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w⋅w
 
@@ -89,14 +89,14 @@ ode_cache = allocate_cache(odeop)
 vθ = similar(u0)
 nl_cache = nothing
 
-odes.θ == 0.0 ? dtθ = dt : dtθ = dt*odes.θ
+ode_solver.θ == 0.0 ? dtθ = dt : dtθ = dt*ode_solver.θ
 tθ = t0+dtθ
 ode_cache = update_cache!(ode_cache,odeop,tθ)
 
 using GridapODEs.ODETools: ThetaMethodNonlinearOperator
 nlop = ThetaMethodNonlinearOperator(odeop,tθ,dtθ,u0,ode_cache,vθ)
 
-nl_cache = solve!(uf,odes.nls,nlop,nl_cache)
+nl_cache = solve!(uf,ode_solver.nls,nlop,nl_cache)
 uf
 
 K = nl_cache.A
diff --git a/test/TransientFEsTests/StokesEquationAutoDiffTests.jl b/test/TransientFEsTests/StokesEquationAutoDiffTests.jl
index 640f039..487d6d6 100644
--- a/test/TransientFEsTests/StokesEquationAutoDiffTests.jl
+++ b/test/TransientFEsTests/StokesEquationAutoDiffTests.jl
@@ -99,9 +99,9 @@ tF = 1.0
 dt = 0.1
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,xh0,t0,tF)
+sol_t = solve(ode_solver,op,xh0,t0,tF)
 
 l2(w) = w⋅w
 
diff --git a/test/TransientFEsTests/StokesEquationTests.jl b/test/TransientFEsTests/StokesEquationTests.jl
index ddba6ea..b731e71 100644
--- a/test/TransientFEsTests/StokesEquationTests.jl
+++ b/test/TransientFEsTests/StokesEquationTests.jl
@@ -84,9 +84,9 @@ tF = 1.0
 dt = 0.1
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,xh0,t0,tF)
+sol_t = solve(ode_solver,op,xh0,t0,tF)
 
 l2(w) = w⋅w
 
diff --git a/test/TransientFEsTests/Transient2ndOrderFEOperatorsTests.jl b/test/TransientFEsTests/Transient2ndOrderFEOperatorsTests.jl
index 914e478..6d3e507 100644
--- a/test/TransientFEsTests/Transient2ndOrderFEOperatorsTests.jl
+++ b/test/TransientFEsTests/Transient2ndOrderFEOperatorsTests.jl
@@ -68,12 +68,12 @@ vh0_const = interpolate_everywhere(v_const(0.0),U0)
 ah0_const = interpolate_everywhere(a_const(0.0),U0)
 
 ls = LUSolver()
-odes = Newmark(ls,dt,γ,β)
+ode_solver = Newmark(ls,dt,γ,β)
 
-sol_t = solve(odes,op,(uh0,vh0,ah0),t0,tF)
-sol_affine_t = solve(odes,op_affine,(uh0,vh0,ah0),t0,tF)
-sol_const_t = solve(odes,op_const,(uh0,vh0_const,ah0_const),t0,tF)
-sol_const_mat_t = solve(odes,op_const_mat,(uh0,vh0,ah0),t0,tF)
+sol_t = solve(ode_solver,op,(uh0,vh0,ah0),t0,tF)
+sol_affine_t = solve(ode_solver,op_affine,(uh0,vh0,ah0),t0,tF)
+sol_const_t = solve(ode_solver,op_const,(uh0,vh0_const,ah0_const),t0,tF)
+sol_const_mat_t = solve(ode_solver,op_const_mat,(uh0,vh0,ah0),t0,tF)
 
 l2(w) = w*w
 
diff --git a/test/TransientFEsTests/TransientFEOperatorsTests.jl b/test/TransientFEsTests/TransientFEOperatorsTests.jl
index 062aa18..9483657 100644
--- a/test/TransientFEsTests/TransientFEOperatorsTests.jl
+++ b/test/TransientFEsTests/TransientFEOperatorsTests.jl
@@ -60,9 +60,9 @@ U0 = U(0.0)
 uh0 = interpolate_everywhere(u(0.0),U0)
 
 ls = LUSolver()
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 
 l2(w) = w*w
 
@@ -91,14 +91,14 @@ nl_cache = nothing
 
 # tf = t0+dt
 
-odes.θ == 0.0 ? dtθ = dt : dtθ = dt*odes.θ
+ode_solver.θ == 0.0 ? dtθ = dt : dtθ = dt*ode_solver.θ
 tθ = t0+dtθ
 ode_cache = update_cache!(ode_cache,odeop,tθ)
 
 using GridapODEs.ODETools: ThetaMethodNonlinearOperator
 nlop = ThetaMethodNonlinearOperator(odeop,tθ,dtθ,u0,ode_cache,vθ)
 
-nl_cache = solve!(uf,odes.nls,nlop,nl_cache)
+nl_cache = solve!(uf,ode_solver.nls,nlop,nl_cache)
 
 K = nl_cache.A
 h = nl_cache.b
diff --git a/test/TransientFEsTests/TransientFETests.jl b/test/TransientFEsTests/TransientFETests.jl
index 779d03a..fb1a66e 100644
--- a/test/TransientFEsTests/TransientFETests.jl
+++ b/test/TransientFEsTests/TransientFETests.jl
@@ -112,16 +112,15 @@ tol = 1.0
 maxiters = 20
 using Gridap.Algebra: NewtonRaphsonSolver
 nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(nls,dt,1.0)
-@test test_transient_fe_solver(odes,op,uh0,t0,tF)
+ode_solver = ThetaMethod(nls,dt,1.0)
+@test test_transient_fe_solver(ode_solver,op,uh0,t0,tF)
 
 residual!(r,op,0.1,(uh,uh),cache)
 jacobian!(J,op,1.0,(uh,uh10),1,1.0,cache)
 jacobian!(J,op,1.0,(uh,uh10),2,10.0,cache)
 
 u0 = get_free_dof_values(uh0)
-odes
-solver = odes
+solver = ode_solver
 t0 = 0.0
 ode_cache = allocate_cache(odeop)
 cache = nothing
@@ -194,7 +193,7 @@ Gridap.Algebra.nlsolve(df,x;linsolve=linsolve!,nls.kwargs...)
 
 using Gridap.FESpaces: get_algebraic_operator
 odeop = get_algebraic_operator(op)
-sol_ode_t = solve(odes,odeop,u0,t0,tF)
+sol_ode_t = solve(ode_solver,odeop,u0,t0,tF)
 
 test_ode_solution(sol_ode_t)
 _t_n = t0
@@ -205,8 +204,8 @@ for (u_n, t_n) in sol_ode_t
   @test all(u_n .≈ t_n)
 end
 
-odes = ThetaMethod(nls,dt,θ)
-sol_ode_t = solve(odes,odeop,u0,t0,tF)
+ode_solver = ThetaMethod(nls,dt,θ)
+sol_ode_t = solve(ode_solver,odeop,u0,t0,tF)
 test_ode_solution(sol_ode_t)
 _t_n = t0
 un, tn = Base.iterate(sol_ode_t)
@@ -217,7 +216,7 @@ for (u_n, t_n) in sol_ode_t
   @test all(u_n .≈ t_n)
 end
 
-sol_t = solve(odes,op,uh0,t0,tF)
+sol_t = solve(ode_solver,op,uh0,t0,tF)
 @test test_transient_fe_solution(sol_t)
 
 _t_n = 0.0
diff --git a/test/TransientFEsTests/VectorHeatEquationTests.jl b/test/TransientFEsTests/VectorHeatEquationTests.jl
index 9bf2892..7dc2660 100644
--- a/test/TransientFEsTests/VectorHeatEquationTests.jl
+++ b/test/TransientFEsTests/VectorHeatEquationTests.jl
@@ -67,9 +67,9 @@ xh0 = interpolate_everywhere([uh0,uh0],X0)
 ls = LUSolver()
 # using Gridap.Algebra: NewtonRaphsonSolver
 # nls = NLSolver(ls;show_trace=true,method=:newton) #linesearch=BackTracking())
-odes = ThetaMethod(ls,dt,θ)
+ode_solver = ThetaMethod(ls,dt,θ)
 
-sol_t = solve(odes,op,xh0,t0,tF)
+sol_t = solve(ode_solver,op,xh0,t0,tF)
 
 l2(w) = w⋅w