qutip · albertomercurio · Apr 6, 2025 · Apr 5, 2025 · Apr 6, 2025
diff --git a/src/entropy.jl b/src/entropy.jl
@@ -55,7 +55,7 @@ function entropy_vn(
     length(indexes) == 0 && return zero(real(T))
     nzvals = vals[indexes]
     logvals = base != 0 ? log.(base, Complex.(nzvals)) : log.(Complex.(nzvals))
-    return -real(mapreduce(*, +, nzvals, logvals))
+    return -real(mapreduce(*,+,nzvals,logvals))
 end
 
 @doc raw"""

diff --git a/src/qobj/eigsolve.jl b/src/qobj/eigsolve.jl
@@ -225,7 +225,7 @@ function _eigsolve(
 
         # println( A * view(V, :, 1:k) ≈ view(V, :, 1:k) * M(view(H, 1:k, 1:k)) + qₘ * M(transpose(view(transpose(βeₘ) * Uₘ, 1:k))) )     # SHOULD BE TRUE
 
-        for j in k+1:m
+        for j in (k+1):m
             β = arnoldi_step!(A, V, H, j)
             if β < tol
                 numops += j - k - 1
@@ -406,15 +406,14 @@ function eigsolve_al(
     kwargs...,
 ) where {HOpType<:Union{OperatorQuantumObject,SuperOperatorQuantumObject}}
     L_evo = _mesolve_make_L_QobjEvo(H, c_ops)
-    prob =
-        mesolveProblem(
-            L_evo,
-            QuantumObject(ρ0, type = Operator, dims = H.dimensions),
-            [zero(T), T];
-            params = params,
-            progress_bar = Val(false),
-            kwargs...,
-        ).prob
+    prob = mesolveProblem(
+        L_evo,
+        QuantumObject(ρ0, type = Operator, dims = H.dimensions),
+        [zero(T), T];
+        params = params,
+        progress_bar = Val(false),
+        kwargs...,
+    ).prob
     integrator = init(prob, alg)
 
     Lmap = ArnoldiLindbladIntegratorMap(eltype(H), size(L_evo), integrator)

diff --git a/src/qobj/operators.jl b/src/qobj/operators.jl
@@ -100,7 +100,7 @@ julia> fock(20, 3)' * a * fock(20, 4)
 2.0 + 0.0im
 ```
 """
-destroy(N::Int) = QuantumObject(spdiagm(1 => Array{ComplexF64}(sqrt.(1:N-1))), Operator, N)
+destroy(N::Int) = QuantumObject(spdiagm(1 => Array{ComplexF64}(sqrt.(1:(N-1)))), Operator, N)
 
 @doc raw"""
     create(N::Int)
@@ -126,7 +126,7 @@ julia> fock(20, 4)' * a_d * fock(20, 3)
 2.0 + 0.0im
 ```
 """
-create(N::Int) = QuantumObject(spdiagm(-1 => Array{ComplexF64}(sqrt.(1:N-1))), Operator, N)
+create(N::Int) = QuantumObject(spdiagm(-1 => Array{ComplexF64}(sqrt.(1:(N-1)))), Operator, N)
 
 @doc raw"""
     displace(N::Int, α::Number)
@@ -167,7 +167,7 @@ Bosonic number operator with Hilbert space cutoff `N`.
 
 This operator is defined as ``\hat{N}=\hat{a}^\dagger \hat{a}``, where ``\hat{a}`` is the bosonic annihilation operator.
 """
-num(N::Int) = QuantumObject(spdiagm(0 => Array{ComplexF64}(0:N-1)), Operator, N)
+num(N::Int) = QuantumObject(spdiagm(0 => Array{ComplexF64}(0:(N-1))), Operator, N)
 
 @doc raw"""
     position(N::Int)
@@ -311,11 +311,11 @@ end
 jmat(j::Real, ::Val{T}) where {T} = throw(ArgumentError("Invalid spin operator: $(T)"))
 
 function _jm(j::Real)
-    m = j:(-1):-j
-    data = sqrt.(j * (j + 1) .- m .* (m .- 1))[1:end-1]
+    m = j:(-1):(-j)
+    data = sqrt.(j * (j + 1) .- m .* (m .- 1))[1:(end-1)]
     return spdiagm(-1 => Array{ComplexF64}(data))
 end
-_jz(j::Real) = spdiagm(0 => Array{ComplexF64}(j .- (0:Int(2 * j))))
+_jz(j::Real) = spdiagm(0 => Array{ComplexF64}(j .- (0:Int(2*j))))
 
 @doc raw"""
     spin_Jx(j::Real)

diff --git a/src/qobj/states.jl b/src/qobj/states.jl
@@ -127,7 +127,7 @@ Density matrix for a thermal state (generating thermal state probabilities) with
 """
 function thermal_dm(N::Int, n::Real; sparse::Union{Bool,Val} = Val(false))
     β = log(1.0 / n + 1.0)
-    N_list = Array{Float64}(0:N-1)
+    N_list = Array{Float64}(0:(N-1))
     data = exp.(-β .* N_list)
     if getVal(sparse)
         return QuantumObject(spdiagm(0 => data ./ sum(data)), Operator, N)

diff --git a/src/spin_lattice.jl b/src/spin_lattice.jl
@@ -53,11 +53,11 @@ function multisite_operator(dims::Union{AbstractVector,Tuple}, pairs::Pair{<:Int
 
     _dims[sites] == [get_dimensions_to(op)[1].size for op in ops] || throw(ArgumentError("The dimensions of the operators do not match the dimensions of the lattice."))
 
-    data = kron(I(prod(_dims[1:sites[1]-1])), ops[1].data)
+    data = kron(I(prod(_dims[1:(sites[1]-1)])), ops[1].data)
     for i in 2:length(sites)
-        data = kron(data, I(prod(_dims[sites[i-1]+1:sites[i]-1])), ops[i].data)
+        data = kron(data, I(prod(_dims[(sites[i-1]+1):(sites[i]-1)])), ops[i].data)
     end
-    data = kron(data, I(prod(_dims[sites[end]+1:end])))
+    data = kron(data, I(prod(_dims[(sites[end]+1):end])))
 
     return QuantumObject(data; type = Operator, dims = dims)
 end

diff --git a/src/steadystate.jl b/src/steadystate.jl
@@ -367,7 +367,7 @@ function _steadystate_fourier(
     N = size(L_0_mat, 1)
     Ns = isqrt(N)
     n_fourier = 2 * n_max + 1
-    n_list = -n_max:n_max
+    n_list = (-n_max):n_max
 
     weight = 1
     Mn = sparse(ones(Ns), [Ns * (j - 1) + j for j in 1:Ns], fill(weight, Ns), N, N)
@@ -399,15 +399,15 @@ function _steadystate_fourier(
 
     offset1 = n_max * N
     offset2 = (n_max + 1) * N
-    ρ0 = reshape(ρtot[offset1+1:offset2], Ns, Ns)
+    ρ0 = reshape(ρtot[(offset1+1):offset2], Ns, Ns)
     ρ0_tr = tr(ρ0)
     ρ0 = ρ0 / ρ0_tr
     ρ0 = QuantumObject((ρ0 + ρ0') / 2, type = Operator, dims = L_0.dimensions)
     ρtot = ρtot / ρ0_tr
 
     ρ_list = [ρ0]
-    for i in 0:n_max-1
-        ρi_m = reshape(ρtot[offset1-(i+1)*N+1:offset1-i*N], Ns, Ns)
+    for i in 0:(n_max-1)
+        ρi_m = reshape(ρtot[(offset1-(i+1)*N+1):(offset1-i*N)], Ns, Ns)
         ρi_m = QuantumObject(ρi_m, type = Operator, dims = L_0.dimensions)
         push!(ρ_list, ρi_m)
     end

diff --git a/src/time_evolution/lr_mesolve.jl b/src/time_evolution/lr_mesolve.jl
@@ -55,9 +55,9 @@
     Δt = 0.0,
 )
 
-#=======================================================#
-#                  ADDITIONAL FUNCTIONS
-#=======================================================#
+#=
+                   ADDITIONAL FUNCTIONS
+=#
 
 select(x::Real, xarr::AbstractArray, retval = false) = retval ? xarr[argmin(abs.(x .- xarr))] : argmin(abs.(x .- xarr))
 
@@ -133,9 +133,9 @@
     end
 end
 
-#=======================================================#
-#                   SAVING FUNCTIONS
-#=======================================================#
+#=
+                    SAVING FUNCTIONS
+=#
 
 function _periodicsave_func(integrator)
     ip = integrator.p
@@ -151,8 +151,8 @@
     N, M = ip.N, ip.M
     idx = select(integrator.t, ip.times)
 
-    @views z = reshape(integrator.u[1:N*M], N, M)
-    @views B = reshape(integrator.u[N*M+1:end], M, M)
+    @views z = reshape(integrator.u[1:(N*M)], N, M)
+    @views B = reshape(integrator.u[(N*M+1):end], M, M)
     _calculate_expectation!(ip, z, B, idx)
 
     if integrator.p.opt.progress
@@ -162,9 +162,9 @@
     return u_modified!(integrator, false)
 end
 
-#=======================================================#
-#                CALLBACK FUNCTIONS
-#=======================================================#
+#=
+                 CALLBACK FUNCTIONS
+=#
 
 #=
     _adjM_condition_ratio(u, t, integrator)
@@ -185,8 +185,8 @@
 
     C = ip.A0
     σ = ip.temp_MM
-    @views z = reshape(u[1:N*M], N, M)
-    @views B = reshape(u[N*M+1:end], M, M)
+    @views z = reshape(u[1:(N*M)], N, M)
+    @views B = reshape(u[(N*M+1):end], M, M)
     mul!(C, z, sqrt(B))
     mul!(σ, C', C)
     p = abs.(eigvals(σ))
@@ -232,16 +232,16 @@
     N, M = ip.N, ip.M
 
     @views begin
-        z = Δt > 0 ? reshape(ip.u_save[1:N*M], N, M) : reshape(integrator.u[1:N*M], N, M)
-        B = Δt > 0 ? reshape(ip.u_save[N*M+1:end], M, M) : reshape(integrator.u[N*M+1:end], M, M)
+        z = Δt > 0 ? reshape(ip.u_save[1:(N*M)], N, M) : reshape(integrator.u[1:(N*M)], N, M)
+        B = Δt > 0 ? reshape(ip.u_save[(N*M+1):end], M, M) : reshape(integrator.u[(N*M+1):end], M, M)
         ψ = ip.L_tilde[:, 1]
         normalize!(ψ)
 
         z = hcat(z, ψ)
         B = cat(B, opt.p0, dims = (1, 2))
         resize!(integrator, length(z) + length(B))
         integrator.u[1:length(z)] .= z[:]
-        integrator.u[length(z)+1:end] .= B[:]
+        integrator.u[(length(z)+1):end] .= B[:]
     end
 
     integrator.p = merge(
@@ -277,9 +277,9 @@
     end
 end
 
-#=======================================================#
-#            DYNAMICAL EVOLUTION EQUATIONS
-#=======================================================#
+#=
+             DYNAMICAL EVOLUTION EQUATIONS
+=#
 
 #=
     dBdz!(du, u, p, t)
@@ -305,10 +305,10 @@
     N, M = p.N, p.M
     opt = p.opt
 
-    @views z = reshape(u[1:N*M], N, M)
-    @views dz = reshape(du[1:N*M], N, M)
-    @views B = reshape(u[N*M+1:end], M, M)
-    @views dB = reshape(du[N*M+1:end], M, M)
+    @views z = reshape(u[1:(N*M)], N, M)
+    @views dz = reshape(du[1:(N*M)], N, M)
+    @views B = reshape(u[(N*M+1):end], M, M)
+    @views dB = reshape(du[(N*M+1):end], M, M)
 
     #Assign A0 and S
     mul!(S, z', z)
@@ -352,17 +352,17 @@
     return dB .-= temp_MM
 end
 
-#=======================================================#
-#                  OUTPUT GENNERATION
-#=======================================================#
+#=
+                  OUTPUT GENNERATION
+=#
 
-get_z(u::AbstractArray{T}, N::Integer, M::Integer) where {T} = reshape(view(u, 1:M*N), N, M)
+get_z(u::AbstractArray{T}, N::Integer, M::Integer) where {T} = reshape(view(u, 1:(M*N)), N, M)
 
 get_B(u::AbstractArray{T}, N::Integer, M::Integer) where {T} = reshape(view(u, (M*N+1):length(u)), M, M)
 
-#=======================================================#
-#                   PROBLEM FORMULATION
-#=======================================================#
+#=
+                    PROBLEM FORMULATION
+=#
 
 @doc raw"""
     lr_mesolveProblem(

diff --git a/src/time_evolution/time_evolution.jl b/src/time_evolution/time_evolution.jl
@@ -397,7 +397,7 @@ end
 @generated function update_coefficients!(L::DiffusionOperator, u, p, t)
     ops_types = L.parameters[2].parameters
     N = length(ops_types)
-    quote
+    return quote
         Base.@nexprs $N i -> begin
             update_coefficients!(L.ops[i], u, p, t)
         end
@@ -538,7 +538,7 @@ function _liouvillian_floquet(
     S = -(L_0 - 1im * n_max * ω * I) \ L_p_dense
     T = -(L_0 + 1im * n_max * ω * I) \ L_m_dense
 
-    for n_i in n_max-1:-1:1
+    for n_i in (n_max-1):-1:1
         S = -(L_0 - 1im * n_i * ω * I + L_m * S) \ L_p_dense
         T = -(L_0 + 1im * n_i * ω * I + L_p * T) \ L_m_dense
     end

diff --git a/src/time_evolution/time_evolution_dynamical.jl b/src/time_evolution/time_evolution_dynamical.jl
@@ -39,15 +39,15 @@ function _increase_dims(
 
     if n_d == 1
         ρmat = similar(QO, dims_new[1], dims_new[1])
-        fill!(selectdim(ρmat, 1, dims[1]+1:dims_new[1]), 0)
-        fill!(selectdim(ρmat, 2, dims[1]+1:dims_new[1]), 0)
+        fill!(selectdim(ρmat, 1, (dims[1]+1):dims_new[1]), 0)
+        fill!(selectdim(ρmat, 2, (dims[1]+1):dims_new[1]), 0)
         copyto!(view(ρmat, 1:dims[1], 1:dims[1]), QO)
     else
         ρmat2 = similar(QO, reverse(vcat(dims_new, dims_new))...)
         ρmat = reshape(QO, reverse(vcat(dims, dims))...)
         for i in eachindex(sel)
-            fill!(selectdim(ρmat2, n_d - sel[i] + 1, dims[sel[i]]+1:dims_new[sel[i]]), 0)
-            fill!(selectdim(ρmat2, 2 * n_d - sel[i] + 1, dims[sel[i]]+1:dims_new[sel[i]]), 0)
+            fill!(selectdim(ρmat2, n_d - sel[i] + 1, (dims[sel[i]]+1):dims_new[sel[i]]), 0)
+            fill!(selectdim(ρmat2, 2 * n_d - sel[i] + 1, (dims[sel[i]]+1):dims_new[sel[i]]), 0)
         end
         copyto!(view(ρmat2, reverse!(repeat([1:n for n in dims], 2))...), ρmat)
         ρmat = reshape(ρmat2, prod(dims_new), prod(dims_new))
@@ -77,7 +77,7 @@ function _DFDIncreaseReduceCondition(u, t, integrator)
         pillow_i = pillow_list[i]
         if dim_i < maxdim_i && dim_i > 2 && maxdim_i != 0
             ρi = _ptrace_oper(vec2mat(dfd_ρt_cache), dim_list, SVector(i))[1]
-            @views res = norm(ρi[diagind(ρi)[end-pillow_i:end]], 1) * sqrt(dim_i) / pillow_i
+            @views res = norm(ρi[diagind(ρi)[(end-pillow_i):end]], 1) * sqrt(dim_i) / pillow_i
             if res > tol_list[i]
                 increase_list[i] = true
             elseif res < tol_list[i] * 1e-2 && dim_i > 3

diff --git a/src/wigner.jl b/src/wigner.jl
@@ -166,10 +166,10 @@ function _wigner_laguerre(ρ::AbstractArray, A::AbstractArray, W::AbstractArray,
     if method.parallel
         throw(ArgumentError("Parallel version is not implemented for dense matrices"))
     else
-        for m in 0:M-1
+        for m in 0:(M-1)
             ρmn = ρ[m+1, m+1]
             abs(ρmn) > tol && (@. W += real(ρmn * (-1)^m * _genlaguerre(m, 0, B)))
-            for n in m+1:M-1
+            for n in (m+1):(M-1)
                 ρmn = ρ[m+1, n+1]
                 # Γ_mn = sqrt(gamma(m+1) / gamma(n+1))
                 Γ_mn = sqrt(exp(loggamma(m + 1) - loggamma(n + 1))) # Is this a good trick?
@@ -197,7 +197,7 @@ function _genlaguerre(n::Int, α::Number, x::T) where {T<:BlasFloat}
     α = convert(T, α)
     p0, p1 = one(T), -x + (α + 1)
     n == 0 && return p0
-    for k in 1:n-1
+    for k in 1:(n-1)
         p1, p0 = ((2k + α + 1) / (k + 1) - x / (k + 1)) * p1 - (k + α) / (k + 1) * p0, p1
     end
     return p1

diff --git a/test/core-test/generalized_master_equation.jl b/test/core-test/generalized_master_equation.jl
@@ -15,7 +15,7 @@
     Tlist = [0, 0.0]
 
     E, U, L1 = liouvillian_generalized(H, fields, Tlist, N_trunc = N_trunc, tol = tol)
-    Ω = to_sparse((E'.-E)[1:N_trunc, 1:N_trunc], tol)
+    Ω = to_sparse((E' .- E)[1:N_trunc, 1:N_trunc], tol)
 
     H_d = Qobj(to_sparse((U'*H*U)[1:N_trunc, 1:N_trunc], tol))
     Xp = Qobj(Ω .* to_sparse(triu((U'*(a+a')*U).data[1:N_trunc, 1:N_trunc], 1), tol))
@@ -33,7 +33,7 @@
     Tlist = [0.2, 0.0]
 
     E, U, L1 = liouvillian_generalized(H, fields, Tlist, N_trunc = N_trunc, tol = tol)
-    Ω = to_sparse((E'.-E)[1:N_trunc, 1:N_trunc], tol)
+    Ω = to_sparse((E' .- E)[1:N_trunc, 1:N_trunc], tol)
 
     H_d = Qobj(to_sparse((U'*H*U)[1:N_trunc, 1:N_trunc], tol))
     Xp = Qobj(Ω .* to_sparse(triu((U'*(a+a')*U).data[1:N_trunc, 1:N_trunc], 1), tol))

diff --git a/test/core-test/low_rank_dynamics.jl b/test/core-test/low_rank_dynamics.jl
@@ -17,13 +17,13 @@
         i += 1
         i <= M && (ϕ[i] = multisite_operator(latt, j => sigmap()) * ϕ[1])
     end
-    for k in 1:N_modes-1
-        for l in k+1:N_modes
+    for k in 1:(N_modes-1)
+        for l in (k+1):N_modes
             i += 1
             i <= M && (ϕ[i] = multisite_operator(latt, k => sigmap(), l => sigmap()) * ϕ[1])
         end
     end
-    for i in i+1:M
+    for i in (i+1):M
         ϕ[i] = QuantumObject(rand(ComplexF64, size(ϕ[1])[1]), dims = ϕ[1].dims)
         normalize!(ϕ[i])
     end

diff --git a/test/core-test/steady_state.jl b/test/core-test/steady_state.jl
@@ -68,8 +68,8 @@
     ρ_ss2 =
         steadystate_fourier(H, -1im * 0.5 * H_t, 1im * 0.5 * H_t, 1, c_ops, solver = SSFloquetEffectiveLiouvillian())
 
-    @test abs(sum(sol_me.expect[1, end-100:end]) / 101 - expect(e_ops[1], ρ_ss1)) < 1e-3
-    @test abs(sum(sol_me.expect[1, end-100:end]) / 101 - expect(e_ops[1], ρ_ss2)) < 1e-3
+    @test abs(sum(sol_me.expect[1, (end-100):end]) / 101 - expect(e_ops[1], ρ_ss1)) < 1e-3
+    @test abs(sum(sol_me.expect[1, (end-100):end]) / 101 - expect(e_ops[1], ρ_ss2)) < 1e-3
 
     @testset "Type Inference (steadystate_fourier)" begin
         @inferred steadystate_fourier(