Drop Logging.jl (#205)

Julia 0.7 is having improved logging capabilities, we can drop
Logging.jl.

REQUIRE

@@ -4,7 +4,6 @@ ForwardDiff
 LightXML 0.4
 HDF5 0.7
 Formatting
-Logging
 TimerOutputs
 AbaqusReader
 AsterReader

src/JuliaFEM.jl

@@ -15,11 +15,8 @@ import FEMBase: get_unknown_field_name, get_unknown_field_dimension,
                 assemble!, update!, initialize!
 using FEMBase: get_problems
 
-# from other packages TimerOutputs.jl and Logging.jl
 using TimerOutputs
 export @timeit, print_timer
-using Logging
-export info, debug
 
 import Base: getindex, setindex!, convert, length, size, isapprox,
              similar, start, first, next, done, last, endof, vec,

src/io.jl

@@ -77,7 +77,6 @@ function get_temporal_collection(xdmf::Xdmf)
     domain = find_element(xdmf.xml, "Domain")
     grid = nothing
     if domain == nothing
-        debug("Xdmf: creating new temporal collection")
         domain = new_child(xdmf.xml, "Domain")
         grid = new_child(domain, "Grid")
         set_attribute(grid, "CollectionType", "Temporal")
@@ -299,13 +298,11 @@ function new_dataitem{T,N}(xdmf::Xdmf, data::Array{T,N})
         # Path can be whatever as XML format does not store to HDF at all
         return new_dataitem(xdmf, "/whatever", data)
     else
-        debug("Determining path for HDF file automatically.")
         path = "/DataItem_$(xdmf.hdf_counter)"
         while exists(xdmf.hdf, path)
             xdmf.hdf_counter += 1
             path = "/DataItem_$(xdmf.hdf_counter)"
         end
-        debug("HDF path automatically determined to be $path")
         return new_dataitem(xdmf, path, data)
     end
 end
@@ -348,8 +345,6 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
     if domain == nothing
         info("Xdmf: Domain not found, creating.")
         domain = new_child(xml, "Domain")
-    else
-        debug("Xdmf: Domain already defined, skipping.")
     end
 
     # 2. find for TemporalCollection
@@ -360,8 +355,6 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
         set_attribute(temporal_collection, "GridType", "Collection")
         set_attribute(temporal_collection, "Name", "Time")
         set_attribute(temporal_collection, "CollectionType", "Temporal")
-    else
-        debug("Xdmf: Temporal collection found, skipping.")
     end
 
     # 2.1 make sure that Grid element we found really is TemporalCollection

src/problems_contact.jl

@@ -61,8 +61,6 @@ end
 function assemble!(problem::Problem{Contact}, time::Real)
     if problem.properties.dimension == -1
         problem.properties.dimension = dim = size(first(problem.elements), 1)
-        debug("assuming dimension of mesh tie surface is $dim")
-        debug("if this is wrong set is manually using problem.properties.dimension")
     end
     dimension = Val{problem.properties.dimension}
     finite_sliding = Val{problem.properties.finite_sliding}

src/problems_contact_3d.jl

@@ -164,7 +164,6 @@ function assemble!(problem::Problem{Contact}, slave_element::Element{Tri3}, time
 
         Ae = De*inv(Me)
     
-        debug("Dual basis coeffients = $Ae")
     end
 
     # loop all polygons
@@ -344,7 +343,6 @@ function assemble!(problem::Problem{Contact}, slave_element::Element{Tri6}, time
 
         Ae = De*inv(Me)
     
-        debug("Dual basis coeffients = $Ae")
     end
 
     # split slave element to linear sub-elements and loop
@@ -520,8 +518,6 @@ function assemble!(problem::Problem{Contact}, time::Float64, ::Type{Val{2}}, ::T
 
     maxdim = maximum(size(C1))
     if problem.properties.alpha != 0.0
-        debug("mortar_3d: size C1 = ", size(C1), " max dim = $maxdim")
-        debug("alpha != 0.0, applying transformation D = Dh*T^-1")
         alp = problem.properties.alpha
         Te = [
                 1.0 0.0 0.0 0.0 0.0 0.0
@@ -566,7 +562,6 @@ function assemble!(problem::Problem{Contact}, time::Float64, ::Type{Val{2}}, ::T
     end
 
     tol = problem.properties.drop_tolerance
-    debug("Dropping small values from C1 & C2, tolerace = $tol")
     SparseArrays.droptol!(C1, tol)
     SparseArrays.droptol!(C2, tol)
 
@@ -650,7 +645,6 @@ function assemble!(problem::Problem{Contact}, time::Float64, ::Type{Val{2}}, ::T
     for j in S
         dofs = [3*(j-1)+1, 3*(j-1)+2, 3*(j-1)+3]
         if is_inactive[j] == 1
-            debug("$j is inactive, removing dofs $dofs")
             C1[dofs,:] = 0.0
             C2[dofs,:] = 0.0
             D[dofs,:] = 0.0
@@ -663,7 +657,6 @@ function assemble!(problem::Problem{Contact}, time::Float64, ::Type{Val{2}}, ::T
         dofs = [3*(j-1)+1, 3*(j-1)+2, 3*(j-1)+3]
         tdofs = dofs[[2,3]]
         if (is_active[j] == 1) && (is_slip[j] == 1)
-            debug("$j is in active/slip, removing tangential constraints $tdofs")
             C2[tdofs,:] = 0.0
             g[tdofs] = 0.0
             normal = normals[j]

src/problems_elasticity.jl

@@ -442,7 +442,6 @@ function lsq_fit(problem, elements, field, time)
             volume += w
         end
     end
-    debug("Mass matrix for least-squares fit is assembled. Total volume to fit: $volume")
     A = sparse(A)
     b = sparse(b)
     A = 1/2*(A + A')

src/problems_mortar_3d.jl

@@ -112,7 +112,6 @@ function get_polygon_clip{T}(xs::Vector{T}, xm::Vector{T}, n::T)
     # 1. test is master point inside slave, if yes, add to clip
     for i=1:nm
         if vertex_inside_polygon(xm[i], xs)
-            # debug("1. $(xm[i]) inside S -> push")
             push!(P, xm[i])
         end
     end
@@ -121,7 +120,6 @@ function get_polygon_clip{T}(xs::Vector{T}, xm::Vector{T}, n::T)
     for i=1:ns
         if vertex_inside_polygon(xs[i], xm)
             approx_in(xs[i], P) && continue
-            # debug("2. $(xs[i]) inside M -> push")
             push!(P, xs[i])
         end
     end
@@ -144,7 +142,6 @@ function get_polygon_clip{T}(xs::Vector{T}, xm::Vector{T}, n::T)
             #info("t=$t, q=$q, q ∈ xm ? $(vertex_inside_polygon(q, xm))")
             if vertex_inside_polygon(q, xm)
                 approx_in(q, P) && continue
-                # debug("3. $q inside M -> push")
                 push!(P, q)
             end
         end
@@ -269,7 +266,6 @@ function check_orientation!(P, n)
     np = length(P)
     s = [dot(n, cross(P[i]-C, P[mod(i+1,np)+1]-C)) for i=1:np]
     all(s .< 0) && return
-    # debug("polygon not in ccw order, fixing")
     # project points to new orthogonal basis Q and sort there
     t1 = (P[1]-C)/norm(P[1]-C)
     t2 = cross(n, t1)
@@ -378,7 +374,6 @@ function assemble!{E<:Union{Tri3, Quad4}}(problem::Problem{Mortar}, slave_elemen
 
     # project slave nodes to auxiliary plane (x0, Q)
     xi = get_mean_xi(slave_element)
-    first_slave_element && debug("midpoint xi = $xi")
     N = vec(get_basis(slave_element, xi, time))
     x0 = interpolate(N, X1)
     n0 = interpolate(N, n1)
@@ -388,8 +383,6 @@ function assemble!{E<:Union{Tri3, Quad4}}(problem::Problem{Mortar}, slave_elemen
 
     if props.dual_basis
 
-        debug("Creating dual basis for element $(slave_element.id)")
-
         De = zeros(nsl, nsl)
         Me = zeros(nsl, nsl)
  
@@ -461,15 +454,6 @@ function assemble!{E<:Union{Tri3, Quad4}}(problem::Problem{Mortar}, slave_elemen
         N_P = length(P)
         P_area = sum([norm(1/2*cross(P[i]-P[1], P[mod(i,N_P)+1]-P[1])) for i=2:N_P])
 
-        if first_slave_element
-            debug("Polygon clip info for first slave element:")
-            debug("S = $S")
-            debug("M = $M")
-            debug("P = $P")
-            debug("N_P = $N_P")
-            debug("P_area = $P_area")
-        end
-
         if isapprox(P_area, 0.0)
             info("Polygon P has zero area: $P_area")
             continue
@@ -600,7 +584,6 @@ function assemble!{E<:Union{Tri6}}(problem::Problem{Mortar}, slave_element::Elem
 
             # create auxiliary plane
             xi = get_mean_xi(sub_slave_element)
-            first_slave_element && debug("midpoint xi = $xi")
             N = vec(get_basis(sub_slave_element, xi, time))
             x0 = interpolate(N, X1)
             n0 = interpolate(N, n1)
@@ -683,7 +666,6 @@ function assemble!{E<:Union{Tri6}}(problem::Problem{Mortar}, slave_element::Elem
 
         # create auxiliary plane
         xi = get_mean_xi(sub_slave_element)
-        first_slave_element && debug("midpoint xi = $xi")
         N = vec(get_basis(sub_slave_element, xi, time))
         x0 = interpolate(N, X1)
         n0 = interpolate(N, n1)
@@ -719,15 +701,6 @@ function assemble!{E<:Union{Tri6}}(problem::Problem{Mortar}, slave_element::Elem
                 N_P = length(P)
                 P_area = sum([norm(1/2*cross(P[i]-P[1], P[mod(i,N_P)+1]-P[1])) for i=2:N_P])
 
-                if first_slave_element
-                    debug("Polygon clip info for first slave element:")
-                    debug("S = $S")
-                    debug("M = $M")
-                    debug("P = $P")
-                    debug("N_P = $N_P")
-                    debug("P_area = $P_area")
-                end
-
                 if isapprox(P_area, 0.0)
                     warn("Polygon P has zero area: $P_area")
                     continue
@@ -838,8 +811,6 @@ function assemble!(problem::Problem{Mortar}, time::Real, ::Type{Val{2}}, ::Type{
 
     maxdim = maximum(size(C1))
     if problem.properties.alpha != 0.0
-        debug("mortar_3d: size C1 = ", size(C1), " max dim = $maxdim")
-        debug("alpha != 0.0, applying transformation D = Dh*T^-1")
         alp = problem.properties.alpha
         Te = [
                 1.0 0.0 0.0 0.0 0.0 0.0
@@ -884,14 +855,11 @@ function assemble!(problem::Problem{Mortar}, time::Real, ::Type{Val{2}}, ::Type{
     end
 
     tol = problem.properties.drop_tolerance
-    debug("Dropping small values from C1 & C2, tolerace = $tol")
     SparseArrays.droptol!(C1, tol)
     SparseArrays.droptol!(C2, tol)
 
     problem.assembly.C1 = C1
     problem.assembly.C2 = C2
 
-    debug("area of interface: $area")
-
 end
 

src/solvers.jl

@@ -193,10 +193,6 @@ function solve!(solver::Solver, K, C1, C2, D, f, g, u, la, ::Type{Val{1}})
     B == B2 || return false
     I = setdiff(A, B)
 
-    debug("# A = $(length(A))")
-    debug("# B = $(length(B))")
-    debug("# I = $(length(I))")
-
     if length(B) == 0
         warn("No rows in C2, forget to set Dirichlet boundary conditions to model?")
     else
@@ -307,7 +303,6 @@ function solve!(solver::Solver; empty_assemblies_before_solution=true, symmetric
     if length(fint) > 1
         # kick in generalized alpha rule for time integration
         alpha = solver.alpha
-        debug("Using generalized-α time integration, α=$alpha")
         K = (1-alpha)*K
         C1 = (1-alpha)*C1
         f = (1-alpha)*f + alpha*fint.data[end-1].second
@@ -571,10 +566,6 @@ function has_converged(solver::Solver{Nonlinear})
             # trivial solution
             has_converged = true
         end
-        debug("Details for problem $(problem.name)")
-        debug("Norm: $(norm(problem.assembly.u))")
-        debug("Norm change: $(problem.assembly.u_norm_change)")
-        debug("Has converged? $(has_converged)")
         converged &= has_converged
     end
     return converged

test/test_mortar_2d_contact.jl

@@ -5,9 +5,6 @@ using JuliaFEM
 using JuliaFEM.Preprocess
 using JuliaFEM.Testing
 
-using Logging
-Logging.configure(level=DEBUG)
-
 mesh = Mesh()
 add_node!(mesh, 1, [0.0, 0.0])
 add_node!(mesh, 2, [1.0, 0.0])

test/test_problems_elasticity.jl

@@ -46,7 +46,6 @@ using JuliaFEM.Testing
         a = geom[i]
         b = strain[i]
         c = stress[i]
-        debug("$a -> $b -> $c")
         @test isapprox(b, [-1/3, -1/3, 1.0, 0.0, 0.0, 0.0])
         @test isapprox(c, [0.0, 0.0, 288.0, 0.0, 0.0, 0.0])
     end