mirror of
https://github.com/JuliaFEM/JuliaFEM.jl.git
synced 2026-08-06 04:21:33 +00:00
use AsterReader.jl (#136)
Functions used to read Code Aster file format are now in separate package AsterReader.jl
This commit is contained in:
Jukka Aho
+5
-1
@@ -3,6 +3,10 @@ os:
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- linux
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julia:
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- 0.6
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addons:
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apt:
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packages:
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- hdf5-tools
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notifications:
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email: false
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webhooks:
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@@ -17,4 +21,4 @@ before_script:
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script:
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- julia --color=yes -e 'using PkgTestSuite; test()'
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after_success:
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- julia --color=yes -e 'using PkgTestSuite; deploy()'
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- julia --color=yes -e 'using PkgTestSuite; deploy()'
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Vendored
+2
@@ -3,5 +3,7 @@
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Pkg.clone("https://github.com/JuliaFEM/AbaqusReader.jl.git")
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Pkg.build("AbaqusReader")
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Pkg.clone("https://github.com/JuliaFEM/AsterReader.jl.git")
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Pkg.build("AsterReader")
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Pkg.clone("https://github.com/JuliaFEM/FEMQuad.jl.git")
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Pkg.build("FEMQuad")
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+2
-6
@@ -136,17 +136,13 @@ include("preprocess.jl")
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export create_elements, Mesh, add_node!, add_nodes!, add_element!,
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add_elements!, add_element_to_element_set!, add_node_to_node_set!,
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find_nearest_nodes, find_nearest_node, reorder_element_connectivity!,
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create_node_set_from_element_set!
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create_node_set_from_element_set!, filter_by_element_set
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include("preprocess_abaqus_reader.jl")
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export abaqus_read_mesh, create_surface_elements
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include("preprocess_aster_reader.jl")
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export aster_create_elements, parse_aster_med_file, is_aster_mail_keyword,
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parse_aster_header, aster_parse_nodes, aster_renumber_nodes!,
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aster_renumber_elements!, aster_combine_meshes, aster_read_mesh,
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filter_by_element_set, filter_by_element_id, MEDFile, aster_read_data,
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aster_read_mesh_names, aster_read_node_sets, aster_read_nodes, RMEDFile
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export aster_read_mesh
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end
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+24
-284
@@ -1,206 +1,19 @@
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# This file is a part of JuliaFEM.
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# License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
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using HDF5
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using JuliaFEM
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function aster_parse_nodes(section; strip_characters=true)
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nodes = Dict{Any, Vector{Float64}}()
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has_started = false
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for line in split(section, '\n')
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m = matchall(r"[\w.-]+", line)
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if (length(m) != 1) && (!has_started)
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continue
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end
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if length(m) == 1
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if (m[1] == "COOR_2D") || (m[1] == "COOR_3D")
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has_started = true
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continue
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end
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if m[1] == "FINSF"
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break
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end
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end
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if length(m) == 4
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nid = m[1]
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if strip_characters
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nid = matchall(r"\d", nid)
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nid = parse(Int, nid[1])
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end
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nodes[nid] = float(m[2:end])
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end
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end
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return nodes
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end
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""" Code Aster binary file (.med). """
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type MEDFile
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data :: Dict
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end
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function MEDFile(fn::String)
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return MEDFile(h5read(fn, "/"))
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end
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function get_mesh_names(med::MEDFile)
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return sort(collect(keys(med.data["FAS"])))
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end
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""" Convert vector of Int8 to ASCII string. """
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function to_ascii(data::Vector{Int8})
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return ascii(unsafe_string(pointer(convert(Vector{UInt8}, data))))
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end
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function get_mesh(med::MEDFile, mesh_name::String)
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if !haskey(med.data["FAS"], mesh_name)
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warn("Mesh $mesh_name not found from med file.")
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meshes = get_mesh_names(med)
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all_meshes = join(meshes, ", ")
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warn("Available meshes: $all_meshes")
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error("Mesh $mesh_name not found.")
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end
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return med.data["FAS"][mesh_name]
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end
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""" Return node sets from med file.
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Notes
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-----
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One node set id can have multiple names.
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using AsterReader
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"""
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function get_node_sets(med::MEDFile, mesh_name::String)::Dict{Int64, Vector{String}}
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mesh = get_mesh(med, mesh_name)
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node_sets = Dict{Int64, Vector{String}}(0 => ["NALL"])
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if !haskey(mesh, "NOEUD")
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return node_sets
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end
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for (k, v) in mesh["NOEUD"]
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nset_id = parse(Int, split(k, "_")[2])
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node_sets[nset_id] = collect(to_ascii(d) for d in v["GRO"]["NOM"])
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end
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return node_sets
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end
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Nodes are different order in Code Aster compared to ABAQUS. This is yet
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incomplete mapping between the permutations. Most of this is still a
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great mystery.
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""" Return element sets from med file.
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Notes
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-----
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One element set id can have multiple names.
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# References
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- http://onelab.info/pipermail/gmsh/2008/003850.html
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- http://caelinux.org/wiki/index.php/Proj:UNVConvert
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"""
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function get_element_sets(med::MEDFile, mesh_name::String)::Dict{Int64, Vector{String}}
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mesh = get_mesh(med, mesh_name)
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element_sets = Dict{Int64, Vector{String}}()
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if !haskey(mesh, "ELEME")
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return element_sets
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end
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for (k, v) in mesh["ELEME"]
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elset_id = parse(Int, split(k, '_')[2])
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element_sets[elset_id] = collect(to_ascii(d) for d in v["GRO"]["NOM"])
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end
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return element_sets
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end
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function get_nodes(med::MEDFile, nsets::Dict{Int, Vector{String}}, mesh_name::String)
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increments = keys(med.data["ENS_MAA"][mesh_name])
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@assert length(increments) == 1
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increment = first(increments)
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nodes = med.data["ENS_MAA"][mesh_name][increment]["NOE"]
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node_ids = nodes["NUM"]
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nset_ids = nodes["FAM"]
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nnodes = length(node_ids)
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node_coords = nodes["COO"]
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dim = round(Int, length(node_coords)/nnodes)
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node_coords = reshape(node_coords, nnodes, dim)'
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d = Dict{Int64}{Tuple{Vector{String}, Vector{Float64}}}()
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for i=1:nnodes
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nset = nsets[nset_ids[i]]
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d[node_ids[i]] = (nset, node_coords[:, i])
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end
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return d
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end
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function get_connectivity(med::MEDFile, elsets::Dict{Int64, Vector{String}}, mesh_name::String)
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if !haskey(elsets, 0)
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elsets[0] = ["OTHER"]
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end
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increments = keys(med.data["ENS_MAA"][mesh_name])
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@assert length(increments) == 1
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increment = first(increments)
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all_elements = med.data["ENS_MAA"][mesh_name][increment]["MAI"]
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d = Dict{Int64, Tuple{Symbol, Vector{String}, Vector{Int64}}}()
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for eltype in keys(all_elements)
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elements = all_elements[eltype]
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elset_ids = elements["FAM"]
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element_ids = elements["NUM"]
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nelements = length(element_ids)
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element_connectivity = elements["NOD"]
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element_dim = round(Int, length(element_connectivity)/nelements)
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element_connectivity = reshape(element_connectivity, nelements, element_dim)'
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for i=1:nelements
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eltype = Symbol(eltype)
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elco = element_connectivity[:, i]
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elset = elsets[elset_ids[i]]
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d[element_ids[i]] = (eltype, elset, elco)
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end
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end
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return d
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end
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""" Parse code aster .med file.
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Paramters
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---------
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fn
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file name to parse
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mesh_name :: optional
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mesh name, if several meshes in one file
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Returns
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-------
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Dict containing fields "nodes" and "connectivity".
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"""
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function parse_aster_med_file(fn, mesh_name=nothing)
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med = MEDFile(fn)
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mesh_names = get_mesh_names(med::MEDFile)
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all_meshes = join(mesh_names, ", ")
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if mesh_name == nothing
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length(mesh_names) == 1 || error("several meshes found from med, pick one: $all_meshes")
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mesh_name = mesh_names[1]
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else
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mesh_name in mesh_names || error("Mesh $mesh_name not found from mesh file $fn. Available meshes: $all_meshes")
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end
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debug("Code Aster .med reader info:")
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elsets = get_element_sets(med, mesh_name)
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for (k,v) in elsets
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debug("ELSET $k => $v")
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end
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nsets = get_node_sets(med, mesh_name)
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for (k,v) in nsets
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debug("NSET $k => $v")
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end
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nodes = get_nodes(med, nsets, mesh_name)
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conn = get_connectivity(med, elsets, mesh_name)
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result = Dict("nodes" => nodes, "connectivity" => conn)
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result["nodes"] = nodes
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result["connectivity"] = conn
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return result
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end
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# some glues about ordering, this is still a mystery..
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# http://onelab.info/pipermail/gmsh/2008/003850.html
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# http://caelinux.org/wiki/index.php/Proj:UNVConvert
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#global const med_connectivity = Dict{Symbol, Vector{Int}}(
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# :Tet4 => [3, 2, 1, 4],
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# :Hex8 => [4, 8, 7, 3, 1, 5, 6, 2], # ..?
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# :Tet10 => [3, 2, 1, 4, 6, 5, 7, 10, 9, 8])
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global const med_connectivity = Dict{Symbol, Vector{Int}}(
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const med_connectivity = Dict{Symbol, Vector{Int}}(
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:Tet4 => [4,3,1,2],
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:Tet10 => [4,3,1,2,10,7,8,9,6,5],
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:Pyr5 => [1,4,3,2,5],
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@@ -209,119 +22,46 @@ global const med_connectivity = Dict{Symbol, Vector{Int}}(
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:Hex20 => [4,8,7,3,1,5,6,2,20,15,19,11,12,16,14,10,17,13,18,9],
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:Hex27 => [4,8,7,3,1,5,6,2,20,15,19,11,12,16,14,10,17,13,18,9,24,25,26,23,21,22,27])
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# element names in CA -> element names in JuliaFEM
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global const mapping = Dict(
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"""
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Map element names used in in Code Aster to element names used in in JuliaFEM
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"""
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const med_element_names = Dict{Symbol, Symbol}(
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:PO1 => :Poi1,
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:SE2 => :Seg2,
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:SE3 => :Seg3,
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:SE4 => :Seg4,
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:TR3 => :Tri3,
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:TR6 => :Tri6,
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:TR7 => :Tri7,
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:QU4 => :Quad4,
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:QU8 => :Quad8,
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:QU9 => :Quad9,
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:TE4 => :Tet4,
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:T10 => :Tet10,
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:PE6 => :Wedge6,
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:P15 => :Wedge15,
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:P18 => :Wedge18,
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:HE8 => :Hex8,
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:H20 => :Hex20,
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:H27 => :Hex27,
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:PY5 => :Pyr5,
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:P13 => :Pyr13,
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:P13 => :Pyr13)
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)
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"""
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aster_read_mesh(filename::String, mesh_name=nothing; reorder_element_connectivity=true)
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""" Read code aster mesh and return Mesh. """
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function aster_read_mesh(fn, mesh_name=nothing; reorder_element_connectivity=true)
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result = parse_aster_med_file(fn, mesh_name)
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mesh = Mesh()
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for (nid, (nsets, ncoords)) in result["nodes"]
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add_node!(mesh, nid, ncoords)
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for nset in nsets
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add_node_to_node_set!(mesh, Symbol(nset), nid)
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end
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end
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for (elid, (eltype, elsets, elcon)) in result["connectivity"]
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haskey(mapping, eltype) || error("Code Aster .med reader: element type $eltype not found from mapping")
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add_element!(mesh, elid, mapping[eltype], elcon)
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for elset in elsets
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add_element_to_element_set!(mesh, Symbol(elset), elid)
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end
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Read code aster mesh from file and return Mesh instance. If mesh file contains
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several meshes, a name of mesh must be given. By default elements are reordered
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so that they match to the conventions used in JuliaFEM.
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"""
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function aster_read_mesh(filename::String, mesh_name=nothing; reorder_element_connectivity=true)
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m = AsterReader.aster_read_mesh(filename, mesh_name)
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mesh = Mesh(m)
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for (elid, eltype) in mesh.element_types
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mesh.element_types[elid] = med_element_names[eltype]
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end
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if reorder_element_connectivity
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reorder_element_connectivity!(mesh, med_connectivity)
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end
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return mesh
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end
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""" Code Aster result file (.rmed). """
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type RMEDFile
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data :: Dict
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end
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function RMEDFile(fn::String)
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return RMEDFile(h5read(fn, "/"))
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end
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""" Return nodes from result med file. """
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function aster_read_nodes(rmed::RMEDFile)
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increments = keys(rmed.data["ENS_MAA"]["MAIL"])
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@assert length(increments) == 1
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increment = first(increments)
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nodes = rmed.data["ENS_MAA"]["MAIL"][increment]["NOE"]
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node_names = nodes["NOM"]
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node_coords = nodes["COO"]
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nnodes = length(node_names)
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dim = round(Int, length(node_coords)/nnodes)
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node_coords = reshape(node_coords, nnodes, dim)'
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stripper(node_name) = strip(ascii(unsafe_string(pointer(convert(Vector{UInt8}, node_name)))))
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node_names = map(stripper, node_names)
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# INFO: quite safe assumption is that id is in node name, i.e. N1 => 1, N123 => 123
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node_id(node_name) = parse(matchall(r"\d+", node_name)[1])
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node_ids = map(node_id, node_names)
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nodes = Dict(j => node_coords[:,j] for j in node_ids)
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return nodes
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end
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""" Read nodal field from rmed file. """
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function aster_read_data(rmed::RMEDFile, field_name; field_type=:NODE,
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info_fields=true, node_ids=nothing)
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if contains(field_name, "ELGA")
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field_type = :GAUSS
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end
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if node_ids == nothing
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nodes = aster_read_nodes(rmed)
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node_ids = sort(collect(keys(nodes)))
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end
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|
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if info_fields
|
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field_names = keys(rmed.data["CHA"])
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all_fields = join(field_names, ", ")
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info("results: $all_fields")
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end
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|
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chdata = rmed.data["CHA"]["RESU____$field_name"]
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@assert length(chdata) == 1
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increment = chdata[first(keys(chdata))]
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if field_type == :NODE
|
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data = increment["NOE"]["MED_NO_PROFILE_INTERNAL"]["CO"]
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results = Dict(j => data[j] for j in node_ids)
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else
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error("Unable to read result of type $field_type: not implemented")
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end
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return results
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end
|
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@@ -5,6 +5,7 @@ using JuliaFEM
|
||||
using JuliaFEM.Preprocess
|
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using JuliaFEM.Postprocess
|
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using JuliaFEM.Testing
|
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using AsterReader: RMEDFile, aster_read_nodes, aster_read_data
|
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|
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#=
|
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Two rings, RING1 = inner, RING2 = outer, RINGS combined mesh. Set T=1.0 for
|
||||
|
||||
@@ -6,6 +6,8 @@ using JuliaFEM.Preprocess
|
||||
using JuliaFEM.Postprocess
|
||||
using JuliaFEM.Testing
|
||||
|
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using AsterReader: RMEDFile, aster_read_nodes, aster_read_data
|
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|
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#=
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||||
Two rings, RING1 is inner, RING2 is outer. Inner diameter is from 0.8 .. 0.9 and
|
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outer ring is 0.9 .. 1.0. Contact surface pair is RING1_OUTER <- RING2_INNER.
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|
||||
@@ -45,46 +45,6 @@ end
|
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@test first(nid) == 13
|
||||
end
|
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|
||||
@testset "code aster / parse nodes" begin
|
||||
section = """
|
||||
N9 2.0 3.0 4.0
|
||||
COOR_3D
|
||||
N1 0.0 0.0 0.0
|
||||
N2 1.0 0.0 0.0
|
||||
N3 1.0 1.0 0.0
|
||||
N4 0.0 1.0 0.0
|
||||
N5 0.0 0.0 1.0
|
||||
N6 1.0 0.0 1.0
|
||||
N7 1.0 1.0 1.0
|
||||
N8 0.0 1.0 1.0
|
||||
FINSF
|
||||
absdflasdf
|
||||
N12 3.0 4.0 5.0 6.0
|
||||
N13 3.0 4.0 5.0
|
||||
"""
|
||||
nodes = aster_parse_nodes(section)
|
||||
@test nodes[1] == Float64[0.0, 0.0, 0.0]
|
||||
@test nodes[8] == Float64[0.0, 1.0, 1.0]
|
||||
@test length(nodes) == 8
|
||||
end
|
||||
|
||||
@testset "test reading aster .med file" begin
|
||||
meshfile = joinpath(datadir, "block_2d_1elem_quad4.med")
|
||||
mesh = aster_read_mesh(meshfile)
|
||||
@test length(mesh.element_sets) == 5
|
||||
@test length(mesh.node_sets) == 4
|
||||
@test length(mesh.elements) == 5
|
||||
@test length(mesh.nodes) == 4
|
||||
for elset in [:BLOCK, :TOP, :BOTTOM, :LEFT, :RIGHT]
|
||||
@test haskey(mesh.element_sets, elset)
|
||||
@test length(mesh.element_sets[elset]) == 1
|
||||
end
|
||||
for nset in [:TOP_LEFT, :TOP_RIGHT, :BOTTOM_LEFT, :BOTTOM_RIGHT]
|
||||
@test haskey(mesh.node_sets, nset)
|
||||
@test length(mesh.node_sets[nset]) == 1
|
||||
end
|
||||
end
|
||||
|
||||
@testset "test filter by element set" begin
|
||||
mesh = aster_read_mesh(joinpath(datadir, "block_2d_1elem_quad4.med"))
|
||||
mesh2 = filter_by_element_set(mesh, :BLOCK)
|
||||
@@ -127,30 +87,3 @@ end
|
||||
# @test isapprox(calculate_volume("PYRAMID_PYRAMID5_1", :Pyramid5, ?))
|
||||
# @test isapprox(calculate_volume("PYRAMID_PYRAMID13_1", :Pyramid13, ?))
|
||||
end
|
||||
|
||||
@testset "read nodal field from code aster result file" begin
|
||||
rmedfile = joinpath(datadir, "rings.rmed")
|
||||
rmed = JuliaFEM.Preprocess.RMEDFile(rmedfile)
|
||||
temp = JuliaFEM.Preprocess.aster_read_data(rmed, "TEMP")
|
||||
@test isapprox(temp[15], 1.0)
|
||||
@test isapprox(temp[95], 2.0)
|
||||
end
|
||||
|
||||
using JuliaFEM.Preprocess: MEDFile, get_element_sets
|
||||
|
||||
@testset "test read element sets from med file, issue #111" begin
|
||||
meshfile = joinpath(datadir, "hexmeshOverlappingGroups.med")
|
||||
med = MEDFile(meshfile)
|
||||
element_sets = get_element_sets(med, "Mesh_1")
|
||||
@test element_sets[-10] == ["halfhex", "mosthex"]
|
||||
@test element_sets[-11] == ["halfhex"]
|
||||
end
|
||||
|
||||
using JuliaFEM.Preprocess: aster_read_mesh
|
||||
|
||||
@testset "test read overlapping ets, issue #111" begin
|
||||
mesh_file = joinpath(datadir, "hexmeshOverlappingGroups.med")
|
||||
mesh = aster_read_mesh(mesh_file, "Mesh_1")
|
||||
@test length(mesh.element_sets[:mosthex]) == 273
|
||||
@test length(mesh.element_sets[:halfhex]) == 147
|
||||
end
|
||||
|
||||
Reference in New Issue
Block a user