Merge branch 'master' into kc/local_buffer

2026-09-10 13:17:42 +00:00 · 2019-11-26 15:29:02 +07:00
parent 2aca9f0d0c e821e07723
commit d781b00da1
15 changed files with 155 additions and 56 deletions
@@ -4,8 +4,8 @@ os:
  - linux

 julia:
-  - 0.7
-  - 1.0
+  - 1.2
+  - 1.3
  - nightly

 addons:
@@ -17,5 +17,14 @@ matrix:
   allow_failures:
       - julia: nightly

+jobs:
+    include:
+        - stage: "Documentation"
+          os: linux
+          script:
+            - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+            - julia --project=docs/ docs/make.jl
+          after_success: skip
+
 after_success:
    - julia -e 'cd(Pkg.dir("JuliaFEM")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
@@ -1,6 +1,7 @@
 name = "JuliaFEM"
 uuid = "f80590ac-b429-510a-8a99-e7c46989f22d"
-version = "0.5.0"
+author = ["Jukka Aho <ahojukka5@gmail.com>", "Tero Frondelius <tero.frondelius@gmail.com>", "Olli Väinölä"]
+version = "0.5.1"

 [deps]
 AbaqusReader = "bc6b9049-e460-56d6-94b4-a597b2c0390d"
@@ -19,6 +20,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MortarContact2D = "048d6160-1a0b-53cd-a5b3-316946cc8d80"
 MortarContact2DAD = "c1673bdb-6aff-560b-99da-c78ea6da9af3"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
+REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -29,5 +31,16 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

+[compat]
+HDF5 = "≥ 0.7.0"
+LightXML = "≥ 0.4.0"
+julia = "≥ 1.0"
+
+[extras]
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
 [targets]
-test = ["Test", "Pkg", "Documenter"]
+test = ["Test"]
@@ -95,7 +95,7 @@ Errors should never pass silently.
 If you like using our package, please consider citing our [article](https://rakenteidenmekaniikka.journal.fi/article/view/64224/26397)
 ```
@article{frondelius2017juliafem,
-  title={JuliaFEM - open source solver for both industrial and academia usage},
+  title={Julia{FEM} - open source solver for both industrial and academia usage},
  volume={50}, 
  url={https://rakenteidenmekaniikka.journal.fi/article/view/64224},
  DOI={10.23998/rm.64224},
@@ -1,17 +0,0 @@
-julia 0.7
-FEMBase
-FEMBasis
-FEMQuad
-ForwardDiff
-LightXML 0.4
-HDF5 0.7
-TimerOutputs
-Reexport
-Arpack
-AbaqusReader
-AsterReader
-HeatTransfer
-MortarContact2D
-MortarContact2DAD
-FEMBeam
-Parameters
@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
@@ -5,7 +5,6 @@ using Documenter

 deploydocs(
    repo = "github.com/JuliaFEM/JuliaFEM.jl.git",
-    julia = "1.0",
    target = "build",
    deps = nothing,
    make = nothing)
@@ -254,8 +254,9 @@ PAGES = [
@info("Pages in documentation", PAGES)

 makedocs(modules=[JuliaFEM],
-         format = :html,
+         format = Documenter.HTML(analytics="UA-83590644-1"),
         checkdocs = :all,
-         sitename = "JuliaFEM",
-         analytics = "UA-83590644-1",
+         sitename = "JuliaFEM.jl",
         pages = PAGES)
+
+include("deploy.jl")
@@ -23,7 +23,7 @@
 # Substituting values, one gets accurate solution to be ``p_0 = 3585 \;\mathrm{MPa}`` and
 # ``a = 6.21 \;\mathrm{mm}``.

-using JuliaFEM
+using JuliaFEM, LinearAlgebra

 # Simulation starts by reading the mesh. Model is constructed and meshed using
 # SALOME, thus mesh format is .med. Mesh type is quite simple structure,
@@ -33,7 +33,7 @@ using JuliaFEM
 # need to use `Mesh` in simulation anyway if we figure some other way to define
 # the geometry for elements.

-datadir = Pkg.dir("JuliaFEM", "examples", "2d_hertz_contact")
+datadir = abspath(joinpath(pathof(JuliaFEM), "..", "..", "examples", "2d_hertz_contact"))
 meshfile = joinpath(datadir, "hertz_2d_full.med")
 mesh = aster_read_mesh(meshfile)
 for (elset_name, element_ids) in mesh.element_sets
@@ -153,6 +153,7 @@ Rt = 0.0
 time = 0.0
 for sel in contact_slave_elements
    for ip in get_integration_points(sel)
+        global Rn, Rt
        w = ip.weight*sel(ip, time, Val{:detJ})
        n = sel("normal", ip, time)
        t = sel("tangent", ip, time)
@@ -181,10 +182,11 @@ p0_acc = 3585.0
 for (nid, n) in normal
    lan = dot(n, lambda[nid])
    println("$nid => $lan")
+    global p0
    p0 = max(p0, lan)
 end
-p0 = round(p0, 2)
-rtol = round(norm(p0-p0_acc)/max(p0,p0_acc)*100, 2)
+p0 = round(p0, digits=2)
+rtol = round(norm(p0-p0_acc)/max(p0,p0_acc)*100, digits=2)
 println("Maximum contact pressure p0 = $p0, p0_acc = $p0_acc, rtol = $rtol %")

 # To get rough approximation where does the contact open, we can find the element
@@ -202,6 +204,7 @@ for element in contact_slave_elements
        println("Contact opening element lambda: la1 = $la1, la2 = $la2")
        x11, y11 = X1
        x12, y12 = X2
+        global a_rad
        a_rad = 1/2*abs(x11+x12)
        break
    end
@@ -119,7 +119,7 @@ using TimerOutputs
 export @timeit, print_timer

 import Base: getindex, setindex!, convert, length, size, isapprox,
-             similar, start, first, next, done, last, endof, vec,
+             similar, first, last, vec,
             ==, +, -, *, /, haskey, copy, push!, isempty, empty!,
             append!, read, copy

@@ -328,6 +328,29 @@ global const xdmf_element_mapping = Dict(
        "Wedge15" => "Wedge_15",
        "Hex20" => "Hex_20")

+get_xdmf_element_code(::Element{Poi1}) = 1
+get_xdmf_element_code(::Element{Seg2}) = 2
+# get_xdmf_element_code(::Element{Polygon}) =  3
+get_xdmf_element_code(::Element{Tri3}) = 4
+get_xdmf_element_code(::Element{Quad4}) = 5
+get_xdmf_element_code(::Element{Tet4}) = 6
+get_xdmf_element_code(::Element{Pyr5}) = 7
+get_xdmf_element_code(::Element{Wedge6}) = 8
+get_xdmf_element_code(::Element{Hex8}) = 9
+# get_xdmf_element_code(::Element{Polyhedron}) = 16
+
+get_xdmf_element_code(::Element{Seg3}) = 34
+get_xdmf_element_code(::Element{Quad9}) = 35
+get_xdmf_element_code(::Element{Tri6}) = 36
+get_xdmf_element_code(::Element{Quad8}) = 37
+get_xdmf_element_code(::Element{Tet10}) = 38
+# get_xdmf_element_code(::Element{Pyr13}) = 39
+get_xdmf_element_code(::Element{Wedge15}) = 40
+# get_xdmf_element_code(::Element{Wedge18}) = 41
+get_xdmf_element_code(::Element{Hex20}) = 48
+# get_xdmf_element_code(::Element{Hex24}) = 49
+get_xdmf_element_code(::Element{Hex27}) = 50
+
 """
    get_spatial_collection()

@@ -416,27 +439,48 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
    add_child(geometry, X_dataitem)

    # 5. save topology
-    all_elements = get_elements(problem)
-    nelements = length(all_elements)
-    element_types = unique(map(get_element_type, all_elements))
-    nelement_types = length(element_types)
-    @debug("Xdmf: Saving topology of $nelements elements total, $nelement_types different element types.")
-
-    for element_type in element_types
-        elements = collect(filter_by_element_type(element_type, all_elements))
-        nelements = length(elements)
-        @debug("Xdmf: $nelements elements of type $element_type")
-        sort!(elements, by=get_element_id)
-        element_ids = map(get_element_id, elements)
-        element_conn = map(element -> [node_mapping[j]-1 for j in get_connectivity(element)], elements)
-        element_conn = hcat(element_conn...)
-        element_code = split(string(element_type), ".")[end]
+    mesh_type = "unstructured"
+    if mesh_type == "unstructured"
+        element_conn = Int64[]
+        for element in get_elements(problem)
+            xdmf_element_code = get_xdmf_element_code(element)
+            xdmf_element_code > 0 || continue
+            push!(element_conn, xdmf_element_code)
+            if xdmf_element_code == 2
+                push!(element_conn, length(element))
+            end
+            for j in get_connectivity(element)
+                push!(element_conn, node_mapping[j]-1)
+            end
+        end
        topology_dataitem = new_dataitem(xdmf, element_conn)
-
        topology = new_child(frame, "Topology")
-        set_attribute(topology, "TopologyType", xdmf_element_mapping[element_code])
-        set_attribute(topology, "NumberOfElements", length(elements))
+        set_attribute(topology, "TopologyType", "Mixed")
        add_child(topology, topology_dataitem)
+    else
+        all_elements = get_elements(problem)
+        nelements = length(all_elements)
+        element_types = unique(map(get_element_type, all_elements))
+        nelement_types = length(element_types)
+        @debug("Xdmf: Saving topology of $nelements elements total, $nelement_types different element types.")
+        if nelement_types != 1
+            error("Xdmf: only single type of element supported by structured grid type!")
+        end
+        for element_type in element_types
+            elements = collect(filter_by_element_type(element_type, all_elements))
+            nelements = length(elements)
+            @debug("Xdmf: $nelements elements of type $element_type")
+            sort!(elements, by=get_element_id)
+            element_ids = map(get_element_id, elements)
+            element_conn = map(element -> [node_mapping[j]-1 for j in get_connectivity(element)], elements)
+            element_conn = hcat(element_conn...)
+            element_code = split(string(element_type), ".")[end]
+            topology_dataitem = new_dataitem(xdmf, element_conn)
+            topology = new_child(frame, "Topology")
+            set_attribute(topology, "TopologyType", xdmf_element_mapping[element_code])
+            set_attribute(topology, "NumberOfElements", length(elements))
+            add_child(topology, topology_dataitem)
+        end
    end

    # 6. save requested fields
@@ -444,7 +488,11 @@ function update_xdmf!(xdmf::Xdmf, problem::Problem, time::Float64, fields::Vecto
        field_dict = problem(field_name, time)
        field_center = "Node"
        field_node_ids = sort(collect(keys(field_dict)))
-        @assert node_ids == field_node_ids
+        if node_ids != field_node_ids
+            @error("geom node ids = $node_ids")
+            @error("field node ids = $field_node_ids")
+            error("!=, geometry does not match with field.")
+        end
        field_dim = length(field_dict[first(field_node_ids)])
        if field_dim == 2
            @debug("Xdmf: Field dimension = 2, extending to 3")
@@ -154,9 +154,39 @@ function allocate_buffer(problem::Problem{Elasticity}, ::Vector{Element{El}}) wh
    nnodes = length(El)
    ndofs = dim*nnodes

+<<<<<<< HEAD
    return Elasticity3DLocalBuffers(ndofs=ndofs, dim=dim, bi = BasisInfo(El))
 end

+=======
+    for element in elements
+
+        u = element("displacement", time)
+        X = element("geometry", time)
+
+        fill!(Km, 0.0)
+        fill!(Kg, 0.0)
+        fill!(f_int, 0.0)
+        fill!(f_ext, 0.0)
+
+        for ip in get_integration_points(element)
+            eval_basis!(bi, X, ip)
+            w = ip.weight*bi.detJ
+            N = bi.N
+            dN = bi.grad  # deriatives of basis functions w.r.t. X, i.e. ∂N/∂X
+            grad!(bi, gradu, u)  # displacement gradient ∇u
+
+            # calculate strain tensor and deformation gradient
+            fill!(strain, 0.0)
+            fill!(F, 0.0)
+            F[:,:] += I
+            if props.finite_strain
+                strain[:,:] = 1/2 * (gradu + gradu' + gradu'*gradu)
+                F[:,:] += gradu
+            else
+                strain[:,:] = 1/2 * (gradu + gradu')
+            end
+>>>>>>> master

 function reset_element!(buf::Elasticity3DLocalBuffers)
    fill!(buf.Km, 0.0)
@@ -175,6 +205,7 @@ function reset_integration_point!(buf::Elasticity3DLocalBuffers)
    return
 end

+<<<<<<< HEAD
 function to_voigt!(strain_vec, strain)
    strain_vec[1] = strain[1,1]
    strain_vec[2] = strain[2,2]
@@ -184,6 +215,16 @@ function to_voigt!(strain_vec, strain)
    strain_vec[6] = 2.0*strain[1,3]
    return
 end
+=======
+            fill!(D, 0.0)
+            E = element("youngs modulus", ip, time)::Float64
+            nu = element("poissons ratio", ip, time)::Float64
+            la = E*nu/((1.0+nu)*(1.0-2.0*nu))
+            mu = E/(2.0*(1.0+nu))
+            D[1,1] = D[2,2] = D[3,3] = 2*mu + la
+            D[4,4] = D[5,5] = D[6,6] = mu
+            D[1,2] = D[2,1] = D[2,3] = D[3,2] = D[1,3] = D[3,1] = la
+>>>>>>> master

 const u = ([0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0])
 const X = ([-93.7197, -93.7197, 150.883], [-91.657, -85.8251, 157.885], [-100.523, -88.8309, 157.883], [-91.6593, -88.8309, 157.883], [-92.6883, -89.7724, 154.384], [-96.0902, -87.328, 157.883], [-97.1216, -91.2753, 154.383], [-92.6895, -91.2753, 154.383], [-91.6581, -87.328, 157.883], [-96.0914, -88.8309, 157.883])
@@ -289,7 +289,7 @@ function update_xdmf!(solver::Solver{Modal})
    # save modes

    temporal_collection = get_temporal_collection(xdmf)
-    unknown_field_name = ucfirst(get_unknown_field_name(solver))
+    unknown_field_name = uppercasefirst(get_unknown_field_name(solver))
    frames = []

    @timeit "save modes" for (j, eigval) in enumerate(real(solver.properties.eigvals))
@@ -1,2 +0,0 @@
-Documenter
-Literate
@@ -3,8 +3,11 @@

 using JuliaFEM, Test

+<<<<<<< HEAD
 # include("../docs/make.jl")

+=======
+>>>>>>> master
@testset "JuliaFEM.jl" begin
    @testset "test_dirichlet.jl" begin
        include("test_dirichlet.jl")
@@ -163,5 +166,3 @@ using JuliaFEM, Test
        include("test_von_mises_material.jl")
    end
 end
-
-include("../docs/deploy.jl")
@@ -34,4 +34,4 @@ eigs_expected = [8809.45, 4936.01, 2880.56, 2491.66, 2004.85,
                 195.832, 104.008, 72.7562, 64.4376, 53.8515,
                 23.8417, 16.6354, 9.54682, 6.93361, 2.22099,
                 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
-@test isapprox(eigs, eigs_expected; atol=1.0e-2)
+@test isapprox(sort(eigs), sort(eigs_expected); atol=1.0e-2)