Merge branch 'master' of https://github.com/JuliaFEM/JuliaFEM.jl

docs/api/empty.txt

@@ -0,0 +1 @@
+

docs/build.jl

@@ -0,0 +1,51 @@
+using Docile, Lexicon, JuliaFEM
+
+const api_directory = "api"
+const modules = [JuliaFEM, JuliaFEM.elasticity_solver]
+
+cd(dirname(@__FILE__)) do
+    # Generate and save the contents of docstrings as markdown files.
+    index  = Index()
+    for mod in modules
+        Lexicon.update!(index, save(joinpath(api_directory, "$(mod).md"), mod))
+    end
+    save(joinpath(api_directory, "index.md"), index; md_subheader = :category)
+
+    # Add a reminder not to edit the generated files.
+    open(joinpath(api_directory, "README_new.md"), "w") do f
+        print(f, """
+        Files in this directory are generated using the `build.jl` script. Make
+        all changes to the originating docstrings/files rather than these ones.
+        """)
+    end
+
+    info("Adding all documentation changes in $(api_directory) to this commit.")
+    success(`git add $(api_directory)`) || exit(1)
+
+end
+
+
+cd(dirname(dirname(@__FILE__))) do
+    yaml = """
+    # This is automatically generated by docs/build.jl. Edit that file if you
+    # wish to make any permenant changes.
+    site_name: JuliaFEM.jl
+    site_description: JuliaFEM.jl, open-source software for reliable, scalable, distributed Finite Element Method.
+    repo_name: GitHub
+    docs_dir: 'docs'
+    site_dir: 'site'
+    repo_url: https://github.com/JuliaFEM/JuliaFEM.jl
+    pages:
+    - Home: 'README.md'
+    - Overview: 'api/index.md'
+    - API Docs:
+      - JuliaFEM: 'api/JuliaFEM.md'
+      - JuliaFEM.elasticity_solver: 'api/JuliaFEM.elasticity_solver.md'
+    """
+
+    # TODO: add the solutions if I figure out how to get them to render properly
+
+    open("mkdocs.yml", "w") do f
+        write(f, yaml)
+    end
+end

src/abaqus_reader.jl

@@ -1,4 +1,6 @@
-# This file is a part of JuliaFEM. License is MIT: https://github.com/ovainola/JuliaFEM/blob/master/README.md
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 module abaqus_reader
 
 using Logging
@@ -6,12 +8,13 @@ using Logging
 
 VERSION < v"0.4-" && using Docile
 
-eldims = Dict("C3D10" => 10)
+eldims = Dict({"C3D10" => 10})
 global handlers = Dict()
 
-"""
+
+@doc """
 Register new handler for parser
-"""
+""" ->
 function add_handler(section, function_name)
   handlers[section] = function_name
 end
@@ -128,5 +131,5 @@ add_handler("NODE", parse_node_section)
 add_handler("ELEMENT", parse_element_section)
 add_handler("NSET", parse_nodeset_section)
 
+end
 
-end

src/elasticity_solver.jl

@@ -1,4 +1,6 @@
-# This file is a part of JuliaFEM. License is MIT: https://github.com/ovainola/JuliaFEM/blob/master/README.md
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 module elasticity_solver
 
 using Logging
@@ -25,11 +27,11 @@ basis :: Function
 ip :: Array{Number, 1}
   Point to interpolate
 """ ->
-function interpolate(field::Array{Float64,1}, basis::Function, ip)
+function interpolate{T<:Real}(field::Array{T,1}, basis::Function, ip)
     result = dot(field, basis(ip))
     return result
 end
-function interpolate(field::Array{Float64,2}, basis::Function, ip)
+function interpolate{T<:Real}(field::Array{T,2}, basis::Function, ip)
     m, n = size(field)
     bip = basis(ip)
     tmp = size(bip)
@@ -63,7 +65,7 @@ end
 @doc """
 Calculate local tangent stiffness matrix and residual force vector R = T - F
 """ ->
-function calc_local_matrices!(X, u, R, Kt, N, dNdξ, λ_, μ_, ipoints, iweights)
+function calc_local_matrices!(X, u, R, Kt, N, dNdchi, lambda_, mu_, ipoints, iweights)
   dim, nnodes = size(X)
   I = eye(dim)
   R[:,:] = 0.0
@@ -73,34 +75,34 @@ function calc_local_matrices!(X, u, R, Kt, N, dNdξ, λ_, μ_, ipoints, iweights
 
   for m = 1:length(iweights)
     w = iweights[m]
-    ξ = ipoints[m, :]
+    chi = ipoints[m, :]
     # interpolate material parameters from element node fields
-    #λ = (λ_*N(ξ))[1]
-    #μ = (μ_*N(ξ))[1]
-    #    Jᵀ = X*dNdξ(ξ)
-    #@debug("Jt:\n",Jᵀ)
-    λ = interpolate(λ_, N, ξ)
-    μ = interpolate(μ_, N, ξ)
-    Jᵀ = interpolate(X, dNdξ, ξ)
-        detJ = det(Jᵀ)
-        ∇N = inv(Jᵀ)*dNdξ(ξ)'
-        ∇u = u*∇N'
-        F = I + ∇u  # Deformation gradient
-        E = 1/2*(∇u' + ∇u + ∇u'*∇u)  # Green-Lagrange strain tensor
-        S = λ*trace(E)*I + 2*μ*E  # PK2 stress tensor
+    #lambda = (lambda_*N(chi))[1]
+    #mu = (mu_*N(chi))[1]
+    #    Jt = X*dNdchi(chi)
+    #@debug("Jt:\n",Jt)
+    lambda = interpolate(lambda_, N, chi)
+    mu = interpolate(mu_, N, chi)
+    Jt = interpolate(X, dNdchi, chi)
+        detJ = det(Jt)
+    deltaN = inv(Jt)*dNdchi(chi)'
+        delta_u = u*deltaN'
+        F = I + delta_u  # Deformation gradient
+        E = 1/2*(delta_u' + delta_u + delta_u'*delta_u)  # Green-Lagrange strain tensor
+        S = lambda*trace(E)*I + 2*mu*E  # PK2 stress tensor
         P = F*S  # PK1 stress tensor
-        R[:,:] += w*P*∇N*detJ
+        R[:,:] += w*P*deltaN*detJ
 
         for p = 1:nnodes
             for i = 1:dim
                 dF[:,:] = 0.0
-                dF[i,:] = ∇N[:,p]
+                dF[i,:] = deltaN[:,p]
                 dE = 1/2*(F'*dF + dF'*F)
-                dS = λ*trace(dE)*I + 2*μ*dE
+                dS = lambda*trace(dE)*I + 2*mu*dE
                 dP = dF*S + F*dS
                 for q = 1:nnodes
                     for j = 1:dim
-                        Kt[dim*(p-1)+i,dim*(q-1)+j] += w*(dP[j,:]*∇N[:,q])[1]*detJ
+                        Kt[dim*(p-1)+i,dim*(q-1)+j] += w*(dP[j,:]*deltaN[:,q])[1]*detJ
                     end
                 end
             end
@@ -212,7 +214,7 @@ Raises
 Exception, if displacement boundary conditions given, i.e.
 DX=2 for some node, for example.
 
-"""
+""" ->
 function eliminate_boundary_conditions(dirichletbc, I, J, V)
     if any(dirichletbc .> 0)
         throw("displacement boundary condition not supported")
@@ -274,7 +276,7 @@ end
 Solve one increment of elasticity problem
 """ ->
 function solve_elasticity_increment!(X, u, du, elmap, nodalloads,
-                                     dirichletbc, λ, μ, N, dNdξ, ipoints,
+                                     dirichletbc, lambda, mu, N, dNdchi, ipoints,
                                      iweights)
     if length(size(elmap)) == 1
         # quick hack for just one element
@@ -297,8 +299,8 @@ function solve_elasticity_increment!(X, u, du, elmap, nodalloads,
     # this can be parallelized
     for i in 1:nelements
         eldofs = elmap[:,i]
-        calc_local_matrices!(X[:, eldofs], u[:, eldofs], R, Kt, N, dNdξ,
-                             λ[eldofs], μ[eldofs], ipoints, iweights)
+        calc_local_matrices!(X[:, eldofs], u[:, eldofs], R, Kt, N, dNdchi,
+                             lambda[eldofs], mu[eldofs], ipoints, iweights)
         assemble!(Kt, eldofs, Imat, Jmat, Vmat)
         assemble!(R, eldofs, Ivec, Vvec)
     end

src/interfaces.jl

@@ -1,4 +1,6 @@
-# This file is a part of JuliaFEM. License is MIT: https://github.com/ovainola/JuliaFEM/blob/master/README.md
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 module interfaces
 
 using Logging
@@ -21,4 +23,4 @@ function solve_elasticity_interface!()
   return 0
 end
 
-end
+end

src/shape_functions.jl

@@ -1,10 +1,8 @@
-function test(a)
-     return a*2
-end
-
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
 function C2D4(xx)
-     θ = 1
+     theta = 1
      chi = xx[1]
      eta = xx[2]
      return = [(1 - chi) * (1 - eta),

src/xdmf.jl

@@ -1,4 +1,6 @@
-# This file is a part of JuliaFEM. License is MIT: https://github.com/ovainola/JuliaFEM/blob/master/README.md
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 module xdmf
 
 using Logging

test/test_abaqus_reader.jl

@@ -1,3 +1,6 @@
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 using FactCheck
 using Logging
 @Logging.configure(level=INFO)
@@ -14,4 +17,4 @@ facts("test import abaqus model") do
     @fact length(model["nsets"]["SUPPORT"]) => 9
     @fact length(model["nsets"]["LOAD"]) => 9
     @fact length(model["nsets"]["TOP"]) => 83
-end
+end

test/test_elasticity_solver.jl

@@ -1,3 +1,6 @@
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 using FactCheck
 using Logging
 @Logging.configure(level=INFO)
@@ -154,6 +157,7 @@ facts("test interpolation of different field variables") do
     F3 = F2'
     F4 = [0.0 0.0; 10.0 0.0; 10.0 1.0; 0.0 1.0]'
     F5 = F4'
+    F6 = [36, 36, 36, 36]
 
     @fact interpolate(F1, N, [0.0, 0.0]) => 36.0
     @fact interpolate(F2, N, [0.0, 0.0]) => 36.0
@@ -161,6 +165,7 @@ facts("test interpolation of different field variables") do
     @fact interpolate(F4, N, [0.0, 0.0]) => [5.0; 0.5]
     @fact interpolate(F5, N, [0.0, 0.0]) => [5.0; 0.5]
     @fact interpolate(F5, dNdξ, [0.0, 0.0]) => [5.0 0.0; 0.0 0.5]
+    @fact interpolate(F6, N, [0.0, 0.0]) => 36
 end
 
 

test/test_model.jl

@@ -1,3 +1,6 @@
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 using FactCheck
 #using JuliaFEM
 using Logging

test/test_xdmf.jl

@@ -1,3 +1,6 @@
+# This file is a part of JuliaFEM.
+# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
+
 using FactCheck
 using Logging
 @Logging.configure(level=INFO)