Merge pull request #2776 from ChrisRackauckas/fix-formatting

Apply JuliaFormatter to fix code formatting

Author: ChrisRackauckas

README.md

@@ -15,7 +15,6 @@ ordinary differential equation solvers and utilities. While completely independe
 and usable on its own, users interested in using this
 functionality should check out [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl).
 
-
 ## Installation
 
 Assuming that you already have Julia correctly installed, it suffices to import

benchmark/benchmarks.jl

@@ -13,8 +13,8 @@ SUITE["nonstiff"] = BenchmarkGroup()
 function lotka_volterra!(du, u, p, t)
     α, β, γ, δ = p
     x, y = u
-    du[1] = α*x - β*x*y  # dx/dt
-    du[2] = δ*x*y - γ*y  # dy/dt
+    du[1] = α * x - β * x * y  # dx/dt
+    du[2] = δ * x * y - γ * y  # dy/dt
     nothing
 end
 
@@ -33,24 +33,24 @@ function pleiades!(du, u, p, t)
     y = @view u[8:14]
     vx = @view u[15:21]
     vy = @view u[22:28]
-    
+
     # Copy velocities to position derivatives
     du[1:7] .= vx
     du[8:14] .= vy
-    
+
     # Calculate accelerations
     fill!(du[15:21], 0.0)
     fill!(du[22:28], 0.0)
-    
+
     for i in 1:7
         for j in 1:7
             if i != j
                 dx = x[j] - x[i]
                 dy = y[j] - y[i]
                 r = sqrt(dx^2 + dy^2)
                 r3 = r^3
-                du[14+i] += j * dx / r3  # mass j = j
-                du[21+i] += j * dy / r3
+                du[14 + i] += j * dx / r3  # mass j = j
+                du[21 + i] += j * dy / r3
             end
         end
     end
@@ -59,8 +59,8 @@ end
 
 function pleiades_prob()
     # Initial conditions from literature
-    u0 = [3.0,3.0,-1.0,-3.0,2.0,-2.0,2.0,3.0,-3.0,2.0,0,0,-4.0,4.0,
-          0,0,0,0,0,1.75,-1.5,0,0,0,-1.25,1,0,0]
+    u0 = [3.0, 3.0, -1.0, -3.0, 2.0, -2.0, 2.0, 3.0, -3.0, 2.0, 0, 0, -4.0, 4.0,
+        0, 0, 0, 0, 0, 1.75, -1.5, 0, 0, 0, -1.25, 1, 0, 0]
     tspan = (0.0, 3.0)
     ODEProblem(pleiades!, u0, tspan)
 end
@@ -69,8 +69,8 @@ end
 function fitzhugh_nagumo!(du, u, p, t)
     a, b, c = p
     v, w = u
-    du[1] = c * (v - v^3/3 + w)    # dv/dt
-    du[2] = -(v - a + b*w) / c     # dw/dt
+    du[1] = c * (v - v^3 / 3 + w)    # dv/dt
+    du[2] = -(v - a + b * w) / c     # dw/dt
     nothing
 end
 
@@ -91,9 +91,9 @@ SUITE["stiff"] = BenchmarkGroup()
 function rober!(du, u, p, t)
     k1, k2, k3 = p
     y1, y2, y3 = u
-    du[1] = -k1*y1 + k3*y2*y3         # dy1/dt
-    du[2] = k1*y1 - k2*y2^2 - k3*y2*y3   # dy2/dt
-    du[3] = k2*y2^2                   # dy3/dt
+    du[1] = -k1 * y1 + k3 * y2 * y3         # dy1/dt
+    du[2] = k1 * y1 - k2 * y2^2 - k3 * y2 * y3   # dy2/dt
+    du[3] = k2 * y2^2                   # dy3/dt
     nothing
 end
 
@@ -109,7 +109,7 @@ function van_der_pol!(du, u, p, t)
     μ = p[1]
     x, y = u
     du[1] = y                      # dx/dt
-    du[2] = μ * ((1 - x^2)*y - x)  # dy/dt
+    du[2] = μ * ((1 - x^2) * y - x)  # dy/dt
     nothing
 end
 
@@ -121,96 +121,95 @@ function van_der_pol_prob()
 end
 
 # Pollution Problem (atmospheric chemistry, 20D stiff system)
-const k1=.35e0
-const k2=.266e2
-const k3=.123e5
-const k4=.86e-3
-const k5=.82e-3
-const k6=.15e5
-const k7=.13e-3
-const k8=.24e5
-const k9=.165e5
-const k10=.9e4
-const k11=.22e-1
-const k12=.12e5
-const k13=.188e1
-const k14=.163e5
-const k15=.48e7
-const k16=.35e-3
-const k17=.175e-1
-const k18=.1e9
-const k19=.444e12
-const k20=.124e4
-const k21=.21e1
-const k22=.578e1
-const k23=.474e-1
-const k24=.178e4
-const k25=.312e1
+const k1 = .35e0
+const k2 = .266e2
+const k3 = .123e5
+const k4 = .86e-3
+const k5 = .82e-3
+const k6 = .15e5
+const k7 = .13e-3
+const k8 = .24e5
+const k9 = .165e5
+const k10 = .9e4
+const k11 = .22e-1
+const k12 = .12e5
+const k13 = .188e1
+const k14 = .163e5
+const k15 = .48e7
+const k16 = .35e-3
+const k17 = .175e-1
+const k18 = .1e9
+const k19 = .444e12
+const k20 = .124e4
+const k21 = .21e1
+const k22 = .578e1
+const k23 = .474e-1
+const k24 = .178e4
+const k25 = .312e1
 
 function pollution!(dy, y, p, t)
-    r1  = k1 *y[1]
-    r2  = k2 *y[2]*y[4]
-    r3  = k3 *y[5]*y[2]
-    r4  = k4 *y[7]
-    r5  = k5 *y[7]
-    r6  = k6 *y[7]*y[6]
-    r7  = k7 *y[9]
-    r8  = k8 *y[9]*y[6]
-    r9  = k9 *y[11]*y[2]
-    r10 = k10*y[11]*y[1]
-    r11 = k11*y[13]
-    r12 = k12*y[10]*y[2]
-    r13 = k13*y[14]
-    r14 = k14*y[1]*y[6]
-    r15 = k15*y[3]
-    r16 = k16*y[4]
-    r17 = k17*y[4]
-    r18 = k18*y[16]
-    r19 = k19*y[16]
-    r20 = k20*y[17]*y[6]
-    r21 = k21*y[19]
-    r22 = k22*y[19]
-    r23 = k23*y[1]*y[4]
-    r24 = k24*y[19]*y[1]
-    r25 = k25*y[20]
-
-    dy[1]  = -r1-r10-r14-r23-r24+
-             r2+r3+r9+r11+r12+r22+r25
-    dy[2]  = -r2-r3-r9-r12+r1+r21
-    dy[3]  = -r15+r1+r17+r19+r22
-    dy[4]  = -r2-r16-r17-r23+r15
-    dy[5]  = -r3+r4+r4+r6+r7+r13+r20
-    dy[6]  = -r6-r8-r14-r20+r3+r18+r18
-    dy[7]  = -r4-r5-r6+r13
-    dy[8]  = r4+r5+r6+r7
-    dy[9]  = -r7-r8
-    dy[10] = -r12+r7+r9
-    dy[11] = -r9-r10+r8+r11
+    r1 = k1 * y[1]
+    r2 = k2 * y[2] * y[4]
+    r3 = k3 * y[5] * y[2]
+    r4 = k4 * y[7]
+    r5 = k5 * y[7]
+    r6 = k6 * y[7] * y[6]
+    r7 = k7 * y[9]
+    r8 = k8 * y[9] * y[6]
+    r9 = k9 * y[11] * y[2]
+    r10 = k10 * y[11] * y[1]
+    r11 = k11 * y[13]
+    r12 = k12 * y[10] * y[2]
+    r13 = k13 * y[14]
+    r14 = k14 * y[1] * y[6]
+    r15 = k15 * y[3]
+    r16 = k16 * y[4]
+    r17 = k17 * y[4]
+    r18 = k18 * y[16]
+    r19 = k19 * y[16]
+    r20 = k20 * y[17] * y[6]
+    r21 = k21 * y[19]
+    r22 = k22 * y[19]
+    r23 = k23 * y[1] * y[4]
+    r24 = k24 * y[19] * y[1]
+    r25 = k25 * y[20]
+
+    dy[1] = -r1 - r10 - r14 - r23 - r24 +
+            r2 + r3 + r9 + r11 + r12 + r22 + r25
+    dy[2] = -r2 - r3 - r9 - r12 + r1 + r21
+    dy[3] = -r15 + r1 + r17 + r19 + r22
+    dy[4] = -r2 - r16 - r17 - r23 + r15
+    dy[5] = -r3 + r4 + r4 + r6 + r7 + r13 + r20
+    dy[6] = -r6 - r8 - r14 - r20 + r3 + r18 + r18
+    dy[7] = -r4 - r5 - r6 + r13
+    dy[8] = r4 + r5 + r6 + r7
+    dy[9] = -r7 - r8
+    dy[10] = -r12 + r7 + r9
+    dy[11] = -r9 - r10 + r8 + r11
     dy[12] = r9
-    dy[13] = -r11+r10
-    dy[14] = -r13+r12
+    dy[13] = -r11 + r10
+    dy[14] = -r13 + r12
     dy[15] = r14
-    dy[16] = -r18-r19+r16
+    dy[16] = -r18 - r19 + r16
     dy[17] = -r20
     dy[18] = r20
-    dy[19] = -r21-r22-r24+r23+r25
-    dy[20] = -r25+r24
+    dy[19] = -r21 - r22 - r24 + r23 + r25
+    dy[20] = -r25 + r24
     nothing
 end
 
 function pollution_prob()
     u0 = zeros(20)
-    u0[2]  = 0.2
-    u0[4]  = 0.04
-    u0[7]  = 0.1
-    u0[8]  = 0.3
-    u0[9]  = 0.01
+    u0[2] = 0.2
+    u0[4] = 0.04
+    u0[7] = 0.1
+    u0[8] = 0.3
+    u0[9] = 0.01
     u0[17] = 0.007
     tspan = (0.0, 60.0)
     ODEProblem(pollution!, u0, tspan)
 end
 
-
 # =============================================================================
 # Scaling Problems (different dimensions)
 # =============================================================================
@@ -243,22 +242,25 @@ limit(a, N) = a == N + 1 ? 1 : a == 0 ? N : a
 function brusselator_2d!(du, u, p, t)
     A, B, α, dx, N = p
     α = α / dx^2
-    
+
     # Create coordinate arrays for this N
     xyd = range(0, stop = 1, length = N)
-    
+
     @inbounds for I in CartesianIndices((N, N))
         i, j = Tuple(I)
         x, y = xyd[i], xyd[j]
-        ip1, im1, jp1, jm1 = limit(i + 1, N), limit(i - 1, N), limit(j + 1, N), limit(j - 1, N)
-        
+        ip1, im1, jp1, jm1 = limit(i + 1, N), limit(i - 1, N), limit(j + 1, N),
+        limit(j - 1, N)
+
         # u equation: ∂u/∂t = 1 + u²v - 4.4u + α∇²u + f(x,y,t)
-        du[i, j, 1] = α * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] - 4*u[i, j, 1]) + 
-                      B + u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] + 
+        du[i, j, 1] = α * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
+                       4 * u[i, j, 1]) +
+                      B + u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] +
                       brusselator_f(x, y, t)
-        
+
         # v equation: ∂v/∂t = 3.4u - u²v + α∇²v  
-        du[i, j, 2] = α * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] - 4*u[i, j, 2]) + 
+        du[i, j, 2] = α * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
+                       4 * u[i, j, 2]) +
                       A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]
     end
     nothing
@@ -270,8 +272,8 @@ function init_brusselator_2d(N::Int)
     for I in CartesianIndices((N, N))
         x = xyd[I[1]]
         y = xyd[I[2]]
-        u[I, 1] = 22 * (y * (1 - y))^(3/2)  # u initial condition
-        u[I, 2] = 27 * (x * (1 - x))^(3/2)  # v initial condition  
+        u[I, 1] = 22 * (y * (1 - y))^(3 / 2)  # u initial condition
+        u[I, 2] = 27 * (x * (1 - x))^(3 / 2)  # v initial condition  
     end
     u
 end
@@ -298,14 +300,17 @@ fn_prob = fitzhugh_nagumo_prob()
 explicit_solvers = [Tsit5(), Vern6(), Vern7(), DP5(), BS3()]
 
 SUITE["nonstiff"]["lotka_volterra"] = BenchmarkGroup()
-SUITE["nonstiff"]["pleiades"] = BenchmarkGroup()  
+SUITE["nonstiff"]["pleiades"] = BenchmarkGroup()
 SUITE["nonstiff"]["fitzhugh_nagumo"] = BenchmarkGroup()
 
 for solver in explicit_solvers
     solver_name = string(typeof(solver).name.name)
-    SUITE["nonstiff"]["lotka_volterra"][solver_name] = @benchmarkable solve($lv_prob, $solver, reltol=1e-6, abstol=1e-8)
-    SUITE["nonstiff"]["pleiades"][solver_name] = @benchmarkable solve($pl_prob, $solver, reltol=1e-6, abstol=1e-8)
-    SUITE["nonstiff"]["fitzhugh_nagumo"][solver_name] = @benchmarkable solve($fn_prob, $solver, reltol=1e-6, abstol=1e-8)
+    SUITE["nonstiff"]["lotka_volterra"][solver_name] = @benchmarkable solve(
+        $lv_prob, $solver, reltol = 1e-6, abstol = 1e-8)
+    SUITE["nonstiff"]["pleiades"][solver_name] = @benchmarkable solve(
+        $pl_prob, $solver, reltol = 1e-6, abstol = 1e-8)
+    SUITE["nonstiff"]["fitzhugh_nagumo"][solver_name] = @benchmarkable solve(
+        $fn_prob, $solver, reltol = 1e-6, abstol = 1e-8)
 end
 
 # Stiff benchmarks with different solvers
@@ -322,9 +327,12 @@ SUITE["stiff"]["pollution"] = BenchmarkGroup()
 
 for solver in stiff_solvers
     solver_name = string(typeof(solver).name.name)
-    SUITE["stiff"]["rober"][solver_name] = @benchmarkable solve($rober_prob_instance, $solver, reltol=1e-6, abstol=1e-8)
-    SUITE["stiff"]["van_der_pol"][solver_name] = @benchmarkable solve($vdp_prob, $solver, reltol=1e-6, abstol=1e-8)
-    SUITE["stiff"]["pollution"][solver_name] = @benchmarkable solve($pollution_prob_instance, $solver, reltol=1e-6, abstol=1e-8)
+    SUITE["stiff"]["rober"][solver_name] = @benchmarkable solve(
+        $rober_prob_instance, $solver, reltol = 1e-6, abstol = 1e-8)
+    SUITE["stiff"]["van_der_pol"][solver_name] = @benchmarkable solve(
+        $vdp_prob, $solver, reltol = 1e-6, abstol = 1e-8)
+    SUITE["stiff"]["pollution"][solver_name] = @benchmarkable solve(
+        $pollution_prob_instance, $solver, reltol = 1e-6, abstol = 1e-8)
 end
 
 # Scaling benchmarks
@@ -334,14 +342,15 @@ SUITE["scaling"]["brusselator_2d"] = BenchmarkGroup()
 # Linear ODE scaling (different problem sizes)
 for N in [10, 50, 100]
     prob = create_linear_prob(N)
-    SUITE["scaling"]["linear"]["N$N"] = @benchmarkable solve($prob, Tsit5(), reltol=1e-6, abstol=1e-8)
+    SUITE["scaling"]["linear"]["N$N"] = @benchmarkable solve(
+        $prob, Tsit5(), reltol = 1e-6, abstol = 1e-8)
 end
 
 # Brusselator 2D scaling (different grid sizes)
 for N in [8, 16, 32]
     prob = create_brusselator_2d_prob(N)
-    SUITE["scaling"]["brusselator_2d"]["$(N)x$(N)"] = @benchmarkable solve($prob, TRBDF2(), 
-        reltol=1e-4, abstol=1e-6, maxiters=1000)
+    SUITE["scaling"]["brusselator_2d"]["$(N)x$(N)"] = @benchmarkable solve($prob, TRBDF2(),
+        reltol = 1e-4, abstol = 1e-6, maxiters = 1000)
 end
 
 # =============================================================================
@@ -353,4 +362,4 @@ SUITE["construction"] = BenchmarkGroup()
 # Test problem construction overhead
 SUITE["construction"]["lotka_volterra"] = @benchmarkable lotka_volterra_prob()
 SUITE["construction"]["rober"] = @benchmarkable rober_prob()
-SUITE["construction"]["linear_N50"] = @benchmarkable create_linear_prob(50)
+SUITE["construction"]["linear_N50"] = @benchmarkable create_linear_prob(50)