chore: format the whole repo

SciML · Mar 29, 2024 · b0daed7 · b0daed7
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diff --git a/README.md b/README.md
@@ -93,9 +93,9 @@ xs, ys = [infimum(d.domain):(dx / 10):supremum(d.domain) for d in domains]
 analytic_sol_func(x, y) = (sin(pi * x) * sin(pi * y)) / (2pi^2)
 
 u_predict = reshape([first(phi([x, y], res.minimizer)) for x in xs for y in ys],
-                    (length(xs), length(ys)))
+    (length(xs), length(ys)))
 u_real = reshape([analytic_sol_func(x, y) for x in xs for y in ys],
-                 (length(xs), length(ys)))
+    (length(xs), length(ys)))
 diff_u = abs.(u_predict .- u_real)
 
 using Plots

diff --git a/docs/make.jl b/docs/make.jl
@@ -10,13 +10,13 @@ using Plots
 include("pages.jl")
 
 makedocs(sitename = "NeuralPDE.jl",
-         authors = "#",
-         modules = [NeuralPDE],
-         clean = true, doctest = false, linkcheck = true,
-         warnonly = [:missing_docs],
-         format = Documenter.HTML(assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/NeuralPDE/stable/"),
-         pages = pages)
+    authors = "#",
+    modules = [NeuralPDE],
+    clean = true, doctest = false, linkcheck = true,
+    warnonly = [:missing_docs],
+    format = Documenter.HTML(assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/NeuralPDE/stable/"),
+    pages = pages)
 
 deploydocs(repo = "github.com/SciML/NeuralPDE.jl.git";
-           push_preview = true)
+    push_preview = true)
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -1,36 +1,36 @@
 pages = ["index.md",
     "ODE PINN Tutorials" => Any["Introduction to NeuralPDE for ODEs" => "tutorials/ode.md",
-                                "Bayesian PINNs for Coupled ODEs" => "tutorials/Lotka_Volterra_BPINNs.md",
-                                "PINNs DAEs" => "tutorials/dae.md",
-                                "Parameter Estimation with PINNs for ODEs" => "tutorials/ode_parameter_estimation.md",
-                                "Deep Galerkin Method" => "tutorials/dgm.md"
-                                #"examples/nnrode_example.md", # currently incorrect
-                                ],
-    "PDE PINN Tutorials" => Any["Introduction to NeuralPDE for PDEs" => "tutorials/pdesystem.md",
-                                "Bayesian PINNs for PDEs" => "tutorials/low_level_2.md",
-                                "Using GPUs" => "tutorials/gpu.md",
-                                "Defining Systems of PDEs" => "tutorials/systems.md",
-                                "Imposing Constraints" => "tutorials/constraints.md",
-                                "The symbolic_discretize Interface" => "tutorials/low_level.md",
-                                "Optimising Parameters (Solving Inverse Problems)" => "tutorials/param_estim.md",
-                                "Solving Integro Differential Equations" => "tutorials/integro_diff.md",
-                                "Transfer Learning with Neural Adapter" => "tutorials/neural_adapter.md",
-                                "The Derivative Neural Network Approximation" => "tutorials/derivative_neural_network.md"],
+        "Bayesian PINNs for Coupled ODEs" => "tutorials/Lotka_Volterra_BPINNs.md",
+        "PINNs DAEs" => "tutorials/dae.md",
+        "Parameter Estimation with PINNs for ODEs" => "tutorials/ode_parameter_estimation.md",
+        "Deep Galerkin Method" => "tutorials/dgm.md"        #"examples/nnrode_example.md", # currently incorrect
+    ],
+    "PDE PINN Tutorials" => Any[
+        "Introduction to NeuralPDE for PDEs" => "tutorials/pdesystem.md",
+        "Bayesian PINNs for PDEs" => "tutorials/low_level_2.md",
+        "Using GPUs" => "tutorials/gpu.md",
+        "Defining Systems of PDEs" => "tutorials/systems.md",
+        "Imposing Constraints" => "tutorials/constraints.md",
+        "The symbolic_discretize Interface" => "tutorials/low_level.md",
+        "Optimising Parameters (Solving Inverse Problems)" => "tutorials/param_estim.md",
+        "Solving Integro Differential Equations" => "tutorials/integro_diff.md",
+        "Transfer Learning with Neural Adapter" => "tutorials/neural_adapter.md",
+        "The Derivative Neural Network Approximation" => "tutorials/derivative_neural_network.md"],
     "Extended Examples" => Any["examples/wave.md",
-                               "examples/3rd.md",
-                               "examples/ks.md",
-                               "examples/heterogeneous.md",
-                               "examples/linear_parabolic.md",
-                               "examples/nonlinear_elliptic.md",
-                               "examples/nonlinear_hyperbolic.md",
-                               "examples/complex.md"],
+        "examples/3rd.md",
+        "examples/ks.md",
+        "examples/heterogeneous.md",
+        "examples/linear_parabolic.md",
+        "examples/nonlinear_elliptic.md",
+        "examples/nonlinear_hyperbolic.md",
+        "examples/complex.md"],
     "Manual" => Any["manual/ode.md",
-                    "manual/dae.md",
-                    "manual/pinns.md",
-                    "manual/bpinns.md",
-                    "manual/training_strategies.md",
-                    "manual/adaptive_losses.md",
-                    "manual/logging.md",
-                    "manual/neural_adapters.md"],
-    "Developer Documentation" => Any["developer/debugging.md"],
+        "manual/dae.md",
+        "manual/pinns.md",
+        "manual/bpinns.md",
+        "manual/training_strategies.md",
+        "manual/adaptive_losses.md",
+        "manual/logging.md",
+        "manual/neural_adapters.md"],
+    "Developer Documentation" => Any["developer/debugging.md"]
 ]
diff --git a/docs/src/developer/debugging.md b/docs/src/developer/debugging.md
@@ -58,8 +58,8 @@ strategy = NeuralPDE.GridTraining(dx)
 integral = NeuralPDE.get_numeric_integral(strategy, indvars, multioutput, chain, derivative)
 
 _pde_loss_function = NeuralPDE.build_loss_function(eq, indvars, depvars, phi, derivative,
-                                                   integral, multioutput, init_params,
-                                                   strategy)
+    integral, multioutput, init_params,
+    strategy)
 ```
 
 ```
@@ -83,9 +83,9 @@ julia> bc_indvars = NeuralPDE.get_variables(bcs,indvars,depvars)
 
 ```julia
 _bc_loss_functions = [NeuralPDE.build_loss_function(bc, indvars, depvars,
-                                                    phi, derivative, integral, multioutput,
-                                                    init_params, strategy,
-                                                    bc_indvars = bc_indvar)
+                          phi, derivative, integral, multioutput,
+                          init_params, strategy,
+                          bc_indvars = bc_indvar)
                       for (bc, bc_indvar) in zip(bcs, bc_indvars)]
 ```
 
@@ -126,7 +126,7 @@ julia> expr_bc_loss_functions = [NeuralPDE.build_symbolic_loss_function(bc,indva
 
 ```julia
 train_sets = NeuralPDE.generate_training_sets(domains, dx, [eq], bcs, eltypeθ, indvars,
-                                              depvars)
+    depvars)
 pde_train_set, bcs_train_set = train_sets
 ```
 
@@ -145,8 +145,9 @@ julia> bcs_train_set
 ```
 
 ```julia
-pde_bounds, bcs_bounds = NeuralPDE.get_bounds(domains, [eq], bcs, eltypeθ, indvars, depvars,
-                                              NeuralPDE.StochasticTraining(100))
+pde_bounds, bcs_bounds = NeuralPDE.get_bounds(
+    domains, [eq], bcs, eltypeθ, indvars, depvars,
+    NeuralPDE.StochasticTraining(100))
 ```
 
 ```

diff --git a/docs/src/examples/complex.md b/docs/src/examples/complex.md
@@ -17,27 +17,29 @@ function bloch_equations(u, p, t)
     γ = Γ / 2
     ρ₁₁, ρ₂₂, ρ₁₂, ρ₂₁ = u
     d̢ρ = [im * Ω * (ρ₁₂ - ρ₂₁) + Γ * ρ₂₂;
-            -im * Ω * (ρ₁₂ - ρ₂₁) - Γ * ρ₂₂;
-            -(γ + im * Δ) * ρ₁₂ - im * Ω * (ρ₂₂ - ρ₁₁);
-            conj(-(γ + im * Δ) * ρ₁₂ - im * Ω * (ρ₂₂ - ρ₁₁))]
+           -im * Ω * (ρ₁₂ - ρ₂₁) - Γ * ρ₂₂;
+           -(γ + im * Δ) * ρ₁₂ - im * Ω * (ρ₂₂ - ρ₁₁);
+           conj(-(γ + im * Δ) * ρ₁₂ - im * Ω * (ρ₂₂ - ρ₁₁))]
     return d̢ρ
 end
 
 u0 = zeros(ComplexF64, 4)
 u0[1] = 1.0
-time_span = (0.0, 2.0)   
+time_span = (0.0, 2.0)
 parameters = [2.0, 0.0, 1.0]
 
 problem = ODEProblem(bloch_equations, u0, time_span, parameters)
 
 chain = Lux.Chain(
-            Lux.Dense(1, 16, tanh; init_weight = (rng, a...) -> Lux.kaiming_normal(rng, ComplexF64, a...)) , 
-            Lux.Dense(16, 4; init_weight = (rng, a...) -> Lux.kaiming_normal(rng, ComplexF64, a...))
-        )
+    Lux.Dense(1, 16, tanh;
+        init_weight = (rng, a...) -> Lux.kaiming_normal(rng, ComplexF64, a...)),
+    Lux.Dense(
+        16, 4; init_weight = (rng, a...) -> Lux.kaiming_normal(rng, ComplexF64, a...))
+)
 ps, st = Lux.setup(rng, chain)
 
 opt = OptimizationOptimisers.Adam(0.01)
-ground_truth  = solve(problem, Tsit5(), saveat = 0.01)
+ground_truth = solve(problem, Tsit5(), saveat = 0.01)
 alg = NNODE(chain, opt, ps; strategy = StochasticTraining(500))
 sol = solve(problem, alg, verbose = false, maxiters = 5000, saveat = 0.01)
 ```

diff --git a/docs/src/examples/heterogeneous.md b/docs/src/examples/heterogeneous.md
@@ -32,9 +32,9 @@ domains = [x ∈ Interval(0.0, 1.0),
 
 numhid = 3
 chains = [[Lux.Chain(Dense(1, numhid, Lux.σ), Dense(numhid, numhid, Lux.σ),
-                     Dense(numhid, 1)) for i in 1:2]
+               Dense(numhid, 1)) for i in 1:2]
           [Lux.Chain(Dense(2, numhid, Lux.σ), Dense(numhid, numhid, Lux.σ),
-                     Dense(numhid, 1)) for i in 1:2]]
+               Dense(numhid, 1)) for i in 1:2]]
 discretization = NeuralPDE.PhysicsInformedNN(chains, QuadratureTraining())
 
 @named pde_system = PDESystem(eq, bcs, domains, [x, y], [p(x), q(y), r(x, y), s(y, x)])

diff --git a/docs/src/examples/linear_parabolic.md b/docs/src/examples/linear_parabolic.md
@@ -24,7 +24,8 @@ w(t, 1) = \frac{e^{\lambda_1} cos(\frac{x}{a})-e^{\lambda_2}cos(\frac{x}{a})}{\l
 with a physics-informed neural network.
 
 ```@example linear_parabolic
-using NeuralPDE, Lux, ModelingToolkit, Optimization, OptimizationOptimisers, OptimizationOptimJL, LineSearches
+using NeuralPDE, Lux, ModelingToolkit, Optimization, OptimizationOptimisers,
+      OptimizationOptimJL, LineSearches
 using Plots
 using ModelingToolkit: Interval, infimum, supremum
 

diff --git a/docs/src/examples/nonlinear_hyperbolic.md b/docs/src/examples/nonlinear_hyperbolic.md
@@ -33,7 +33,8 @@ where k is a root of the algebraic (transcendental) equation f(k) = g(k), j0 and
 We solve this with Neural:
 
 ```@example nonlinear_hyperbolic
-using NeuralPDE, Lux, ModelingToolkit, Optimization, OptimizationOptimJL, Roots, LineSearches
+using NeuralPDE, Lux, ModelingToolkit, Optimization, OptimizationOptimJL, Roots,
+      LineSearches
 using SpecialFunctions
 using Plots
 using ModelingToolkit: Interval, infimum, supremum
@@ -121,7 +122,6 @@ for i in 1:2
 end
 ```
 
-
 ```@example nonlinear_hyperbolic
 ps[1]
 ```

diff --git a/docs/src/examples/wave.md b/docs/src/examples/wave.md
@@ -70,9 +70,9 @@ function analytic_sol_func(t, x)
 end
 
 u_predict = reshape([first(phi([t, x], res.u)) for t in ts for x in xs],
-                    (length(ts), length(xs)))
+    (length(ts), length(xs)))
 u_real = reshape([analytic_sol_func(t, x) for t in ts for x in xs],
-                 (length(ts), length(xs)))
+    (length(ts), length(xs)))
 
 diff_u = abs.(u_predict .- u_real)
 p1 = plot(ts, xs, u_real, linetype = :contourf, title = "analytic");
@@ -121,7 +121,7 @@ eq = Dx(Dxu(t, x)) ~ 1 / v^2 * Dt(Dtu(t, x)) + b * Dtu(t, x)
 bcs_ = [u(t, 0) ~ 0.0,# for all t > 0
     u(t, L) ~ 0.0,# for all t > 0
     u(0, x) ~ x * (1.0 - x), # for all 0 < x < 1
-    Dtu(0, x) ~ 1 - 2x, # for all  0 < x < 1
+    Dtu(0, x) ~ 1 - 2x # for all  0 < x < 1
 ]
 
 ep = (cbrt(eps(eltype(Float64))))^2 / 6
@@ -139,16 +139,16 @@ domains = [t ∈ Interval(0.0, L),
 inn = 25
 innd = 4
 chain = [[Lux.Chain(Dense(2, inn, Lux.tanh),
-                    Dense(inn, inn, Lux.tanh),
-                    Dense(inn, inn, Lux.tanh),
-                    Dense(inn, 1)) for _ in 1:3]
+              Dense(inn, inn, Lux.tanh),
+              Dense(inn, inn, Lux.tanh),
+              Dense(inn, 1)) for _ in 1:3]
          [Lux.Chain(Dense(2, innd, Lux.tanh), Dense(innd, 1)) for _ in 1:2]]
 
 strategy = GridTraining(0.02)
 discretization = PhysicsInformedNN(chain, strategy;)
 
 @named pde_system = PDESystem(eq, bcs, domains, [t, x],
-                              [u(t, x), Dxu(t, x), Dtu(t, x), O1(t, x), O2(t, x)])
+    [u(t, x), Dxu(t, x), Dtu(t, x), O1(t, x), O2(t, x)])
 prob = discretize(pde_system, discretization)
 sym_prob = NeuralPDE.symbolic_discretize(pde_system, discretization)
 
@@ -201,10 +201,11 @@ gif(anim, "1Dwave_damped_adaptive.gif", fps = 200)
 
 # Surface plot
 ts, xs = [infimum(d.domain):0.01:supremum(d.domain) for d in domains]
-u_predict = reshape([first(phi([t, x], res.u.depvar.u)) for
-                     t in ts for x in xs], (length(ts), length(xs)))
+u_predict = reshape(
+    [first(phi([t, x], res.u.depvar.u)) for
+     t in ts for x in xs], (length(ts), length(xs)))
 u_real = reshape([analytic_sol_func(t, x) for t in ts for x in xs],
-                 (length(ts), length(xs)))
+    (length(ts), length(xs)))
 
 diff_u = abs.(u_predict .- u_real)
 p1 = plot(ts, xs, u_real, linetype = :contourf, title = "analytic");

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,7 +1,7 @@
 # NeuralPDE.jl: Automatic Physics-Informed Neural Networks (PINNs)
 
-[NeuralPDE.jl](https://github.com/SciML/NeuralPDE.jl) is a solver package which 
-consists of neural network solvers for partial differential equations using 
+[NeuralPDE.jl](https://github.com/SciML/NeuralPDE.jl) is a solver package which
+consists of neural network solvers for partial differential equations using
 physics-informed neural networks (PINNs) and the ability to generate neural
 networks which both approximate physical laws and real data simultaneously.
 

diff --git a/docs/src/manual/bpinns.md b/docs/src/manual/bpinns.md
@@ -22,4 +22,3 @@ SciMLBase.symbolic_discretize(::PDESystem, ::NeuralPDE.AbstractPINN)
 NeuralPDE.BPINNstats
 NeuralPDE.BPINNsolution
 ```
-
diff --git a/docs/src/manual/ode.md b/docs/src/manual/ode.md
@@ -8,4 +8,4 @@ NNODE
 
 ```@docs
 BNNODE
-```
+```
diff --git a/docs/src/tutorials/constraints.md b/docs/src/tutorials/constraints.md
@@ -47,9 +47,9 @@ domains = [x ∈ Interval(x_0, x_end)]
 # Neural network
 inn = 18
 chain = Lux.Chain(Dense(1, inn, Lux.σ),
-                  Dense(inn, inn, Lux.σ),
-                  Dense(inn, inn, Lux.σ),
-                  Dense(inn, 1))
+    Dense(inn, inn, Lux.σ),
+    Dense(inn, inn, Lux.σ),
+    Dense(inn, 1))
 
 lb = [x_0]
 ub = [x_end]
@@ -63,8 +63,8 @@ function norm_loss_function(phi, θ, p)
 end
 
 discretization = PhysicsInformedNN(chain,
-                                   QuadratureTraining(),
-                                   additional_loss = norm_loss_function)
+    QuadratureTraining(),
+    additional_loss = norm_loss_function)
 
 @named pdesystem = PDESystem(eq, bcs, domains, [x], [p(x)])
 prob = discretize(pdesystem, discretization)
@@ -84,7 +84,8 @@ cb_ = function (p, l)
     return false
 end
 
-res = Optimization.solve(prob, BFGS(linesearch = BackTracking()), callback = cb_, maxiters = 600)
+res = Optimization.solve(
+    prob, BFGS(linesearch = BackTracking()), callback = cb_, maxiters = 600)
 ```
 
 And some analysis:

diff --git a/docs/src/tutorials/dae.md b/docs/src/tutorials/dae.md
@@ -5,16 +5,14 @@
     It is highly recommended you first read the [solving ordinary differential
     equations with DifferentialEquations.jl tutorial](https://docs.sciml.ai/DiffEqDocs/stable/tutorials/dae_example/) before reading this tutorial.
 
-
-This tutorial is an introduction to using physics-informed neural networks (PINNs) for solving differential algebraic equations (DAEs). 
-
+This tutorial is an introduction to using physics-informed neural networks (PINNs) for solving differential algebraic equations (DAEs).
 
 ## Solving an DAE with PINNs
 
 Let's solve a simple DAE system:
 
 ```@example dae
-using NeuralPDE 
+using NeuralPDE
 using Random
 using OrdinaryDiffEq, Statistics
 using Lux, OptimizationOptimisers
@@ -57,4 +55,4 @@ ground_sol = solve(prob_mm, Rodas5(), reltol = 1e-8, abstol = 1e-8)
 using Plots
 plot(ground_sol, tspan = tspan, layout = (2, 1), label = "ground truth")
 plot!(sol, tspan = tspan, layout = (2, 1), label = "dae with pinns")
-```
+```
diff --git a/docs/src/tutorials/derivative_neural_network.md b/docs/src/tutorials/derivative_neural_network.md
@@ -91,7 +91,8 @@ input_ = length(domains)
 n = 15
 chain = [Lux.Chain(Dense(input_, n, Lux.σ), Dense(n, n, Lux.σ), Dense(n, 1)) for _ in 1:7]
 
-training_strategy = NeuralPDE.QuadratureTraining(; batch = 200, reltol = 1e-6, abstol = 1e-6)
+training_strategy = NeuralPDE.QuadratureTraining(;
+    batch = 200, reltol = 1e-6, abstol = 1e-6)
 discretization = NeuralPDE.PhysicsInformedNN(chain, training_strategy)
 
 vars = [u1(t, x), u2(t, x), u3(t, x), Dxu1(t, x), Dtu1(t, x), Dxu2(t, x), Dtu2(t, x)]
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,4 +22,3 @@ SciMLBase.symbolic_discretize(::PDESystem, ::NeuralPDE.AbstractPINN)
		NeuralPDE.BPINNstats
		NeuralPDE.BPINNsolution
		```
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,4 +8,4 @@ NNODE @@
     ```@docs
     BNNODE
-    ```
+    ```