mirror of
https://github.com/JuliaFEM/JuliaFEM.jl.git
synced 2026-08-06 04:21:33 +00:00
fixed xdmf writer tests + some modifications hwo elements are exported
This commit is contained in:
Jukka Aho
+36
-95
@@ -35,20 +35,12 @@ using LightXML
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# > #define XDMF_3DSMESH 0x1100
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# > #define XDMF_3DRECTMESH 0x1101
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# > #define XDMF_3DCORECTMESH 0x1102
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"""
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Build a new model for outout
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Parameters
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----------
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global eltypes = Dict{Symbol, Int}(
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:Tet4 => 0x6,
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:Quad4 => 0x5,
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:Tet10 => 0x0026)
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Examples
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-------
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```julia
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@assert 1+1 == 3
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```
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"""
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function xdmf_new_model(xdmf_version="2.1")
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xdoc = XMLDocument()
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xroot = create_root(xdoc, "Xdmf")
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@@ -63,11 +55,11 @@ function xdmf_new_temporal_collection(model)
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set_attribute(temporal_collection, "CollectionType", "Temporal")
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set_attribute(temporal_collection, "GridType", "Collection")
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set_attribute(temporal_collection, "Name", "Collection")
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geometry = new_child(temporal_collection, "Geometry")
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set_attribute(geometry, "Type", "None")
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topology = new_child(temporal_collection, "Topology")
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set_attribute(topology, "Dimensions", "0")
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set_attribute(topology, "Type", "NoTopology")
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# geometry = new_child(temporal_collection, "Geometry")
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# set_attribute(geometry, "Type", "None")
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# topology = new_child(temporal_collection, "Topology")
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# set_attribute(topology, "Dimensions", "0")
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# set_attribute(topology, "Type", "NoTopology")
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return temporal_collection
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end
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@@ -79,102 +71,51 @@ function xdmf_new_grid(temporal_collection; time=0)
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return grid
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end
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#function xdmf_new_mesh(grid, X, elmap)
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# geometry = new_child(grid, "Geometry")
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# set_attribute(geometry, "Type", "XYZ")
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# dataitem = new_child(geometry, "DataItem")
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# set_attribute(dataitem, "DataType", "Float")
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# set_attribute(dataitem, "Dimensions", length(X))
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# set_attribute(dataitem, "Format", "XML")
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# set_attribute(dataitem, "Precision", "4")
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# add_text(dataitem, join(X, " "))
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# topology = new_child(grid, "Topology")
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# set_attribute(topology, "Dimensions", "1")
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# set_attribute(topology, "Type", "Mixed")
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# dataitem = new_child(topology, "DataItem")
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# set_attribute(dataitem, "DataType", "Int")
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# set_attribute(dataitem, "Dimensions", length(elmap))
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# set_attribute(dataitem, "Format", "XML")
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# set_attribute(dataitem, "Precision", 4)
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# elmap2 = copy(elmap)
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# elmap2[2:end,:] -= 1
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# add_text(dataitem, join(elmap2, " "))
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#end
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function xdmf_new_mesh!(grid, nodes, elements)
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function xdmf_new_mesh(grid, X, elmap)
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dim, nnodes = size(X)
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# 1. write nodes
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geometry = new_child(grid, "Geometry")
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set_attribute(geometry, "Type", "XYZ")
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dataitem = new_child(geometry, "DataItem")
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set_attribute(dataitem, "DataType", "Float")
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set_attribute(dataitem, "Dimensions", "$nnodes $dim")
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ndim = sum([length(node) for node in nodes])
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info("XDFM: ndim = $ndim")
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set_attribute(dataitem, "Dimensions", "$ndim")
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 8)
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#add_text(dataitem, join(X, " "))
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s = "\n"
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for i=1:nnodes
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s *= "\t\t" * join(X[:,i], " ") * "\n"
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end
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s *= " "
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add_text(dataitem, s)
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elmap2 = copy(elmap)
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elmap2[2:end,:] -= 1
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dim, nelements = size(elmap2)
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s = join([join(node, " ") for node in round(nodes, 5)], "\n")
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add_text(dataitem, "\n"*s*"\n")
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# 2. write elements
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topology = new_child(grid, "Topology")
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#set_attribute(topology, "Dimensions", "1")
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eldim = sum([length(element[2]) for element in elements]) + length(elements)
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set_attribute(topology, "TopologyType", "Mixed")
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set_attribute(topology, "NumberOfElements", nelements)
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set_attribute(topology, "NumberOfElements", length(elements))
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dataitem = new_child(topology, "DataItem")
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set_attribute(dataitem, "DataType", "Int")
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set_attribute(dataitem, "Dimensions", "$nelements $dim")
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 8)
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s = "\n"
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for i=1:nelements
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s *= "\t\t" * join(elmap2[:,i], " ") * "\n"
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end
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add_text(dataitem, s)
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#add_text(dataitem, join(elmap2, " "))
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set_attribute(dataitem, "DataType", "Int")
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set_attribute(dataitem, "Dimensions", "$eldim")
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# set_attribute(dataitem, "Precision", 8)
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# note: id numbers start from 0 in Xdmf
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s = join([join([eltypes[eltype]; connectivity-1], " ") for (eltype, connectivity) in elements], "\n")
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add_text(dataitem, "\n"*s*"\n")
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end
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function xdmf_new_field(grid, name, source, data)
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loc = Dict("elements" => "Cell",
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"nodes" => "Node")
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dim1, dim2 = size(data'')
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if dim1 == 1
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Type = "Scalar"
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end
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if dim1 == 3
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Type = "Vector"
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end
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typ = string(typeof(data))
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datatype = "unknown"
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for j in ["Int", "Float"]
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if contains(typ, j)
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datatype = j
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end
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end
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if datatype == "unknown"
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throw("unknown data type ", typ)
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end
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""" Write Vector field to nodes. """
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function xdmf_new_nodal_field!(grid, name, data)
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attribute = new_child(grid, "Attribute")
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set_attribute(attribute, "Center", loc[source])
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set_attribute(attribute, "Center", "Node")
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set_attribute(attribute, "Name", name)
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set_attribute(attribute, "Type", Type)
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set_attribute(attribute, "Type", "Vector")
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dataitem = new_child(attribute, "DataItem")
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set_attribute(dataitem, "DataType", datatype)
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set_attribute(dataitem, "Dimensions", length(data))
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set_attribute(dataitem, "DataType", "Float")
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ndim = sum([length(d) for d in data])
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set_attribute(dataitem, "Dimensions", "$ndim")
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 4)
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add_text(dataitem, join(data, " "))
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set_attribute(dataitem, "Precision", 8)
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s = join([join(d, " ") for d in round(data, 5)], "\n")
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add_text(dataitem, "\n"*s*"\n")
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end
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function xdmf_save_model(xdoc, filename)
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+104
-108
@@ -1,32 +1,72 @@
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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 FactCheck
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using Logging
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@Logging.configure(level=INFO)
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module XDMFTests
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using LightXML
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using JuliaFEM
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using JuliaFEM.Postprocess
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using JuliaFEM.Test
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testdata = """\
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<?xml version="1.0" encoding="utf-8"?>
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<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.1">
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<Domain>
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<Grid CollectionType="Temporal" GridType="Collection" Name="Collection">
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<Geometry Type="None"/>
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<Topology Dimensions="0" Type="NoTopology"/>
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<Grid Name="Grid">
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<Time Value="123"/>
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<Time Value="123"/>
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<Geometry Type="XYZ">
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<DataItem DataType="Float" Dimensions="12" Format="XML" Precision="4">0 0 0 1 0 0 0 1 0 0 0 1</DataItem>
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<DataItem DataType="Float" Dimensions="60" Format="XML" Precision="8">
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0.0 0.0 0.0
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1.0 0.0 0.0
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0.0 1.0 0.0
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0.0 0.0 1.0
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0.5 0.0 0.0
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0.5 0.5 0.0
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0.0 0.5 0.0
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0.0 0.0 0.5
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0.5 0.0 0.5
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0.0 0.5 0.5
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1.0 1.0 1.0
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2.0 1.0 1.0
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1.0 2.0 1.0
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1.0 1.0 2.0
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1.5 1.0 1.0
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1.5 1.5 1.0
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1.0 1.5 1.0
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1.0 1.0 1.5
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1.5 1.0 1.5
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1.0 1.5 1.5
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</DataItem>
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</Geometry>
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<Topology Dimensions="1" Type="Mixed">
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<DataItem DataType="Int" Dimensions="5" Format="XML" Precision="4">6 0 1 2 3</DataItem>
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<Topology TopologyType="Mixed" NumberOfElements="2" >
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<DataItem Format="XML" DataType="Int" Dimensions="22">
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38 0 1 2 3 4 5 6 7 8 9
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38 10 11 12 13 14 15 16 17 18 19
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</DataItem>
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</Topology>
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<Attribute Center="Cell" Name="Temperature field" Type="Scalar">
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<DataItem DataType="Int" Dimensions="1" Format="XML" Precision="4">56</DataItem>
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</Attribute>
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<Attribute Center="Node" Name="Density" Type="Vector">
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<DataItem DataType="Float" Dimensions="12" Format="XML" Precision="4">1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0</DataItem>
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<Attribute Center="Node" Name="Displacement" Type="Vector">
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<DataItem DataType="Float" Dimensions="60" Format="XML" Precision="8">
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0.0 0.0 0.0
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1.0 0.0 0.0
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0.0 1.0 0.0
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0.0 0.0 1.0
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0.5 0.0 0.0
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0.5 0.5 0.0
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0.0 0.5 0.0
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0.0 0.0 0.5
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0.5 0.0 0.5
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0.0 0.5 0.5
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1.0 1.0 1.0
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2.0 1.0 1.0
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1.0 2.0 1.0
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1.0 1.0 2.0
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1.5 1.0 1.0
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1.5 1.5 1.0
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1.0 1.5 1.0
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1.0 1.0 1.5
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1.5 1.0 1.5
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1.0 1.5 1.5
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</DataItem>
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</Attribute>
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</Grid>
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</Grid>
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@@ -34,100 +74,56 @@ testdata = """\
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</Xdmf>
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"""
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# makes no sense for vector field
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# <DataItem DataType="Float" Dimensions="4" Format="XML" Precision="4">1 2 4 7</DataItem>
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function test_write_to_xml()
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nodes = Vector{Float64}[
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[0.0, 0.0, 0.0],
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[1.0, 0.0, 0.0],
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[0.0, 1.0, 0.0],
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[0.0, 0.0, 1.0],
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[0.5, 0.0, 0.0],
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[0.5, 0.5, 0.0],
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[0.0, 0.5, 0.0],
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[0.0, 0.0, 0.5],
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[0.5, 0.0, 0.5],
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[0.0, 0.5, 0.5],
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[1.0, 1.0, 1.0],
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[2.0, 1.0, 1.0],
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[1.0, 2.0, 1.0],
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[1.0, 1.0, 2.0],
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[1.5, 1.0, 1.0],
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[1.5, 1.5, 1.0],
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[1.0, 1.5, 1.0],
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[1.0, 1.0, 1.5],
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[1.5, 1.0, 1.5],
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[1.0, 1.5, 1.5]]
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facts("test test data") do
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xdoc = XMLDocument()
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xroot = create_root(xdoc, "Xdmf")
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set_attribute(xroot, "xmlns:xi", "http://www.w3.org/2001/XInclude")
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set_attribute(xroot, "Version", "2.1")
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domain = new_child(xroot, "Domain")
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temporal_collection = new_child(domain, "Grid")
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set_attribute(temporal_collection, "CollectionType", "Temporal")
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set_attribute(temporal_collection, "GridType", "Collection")
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set_attribute(temporal_collection, "Name", "Collection")
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geometry = new_child(temporal_collection, "Geometry")
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set_attribute(geometry, "Type", "None")
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topology = new_child(temporal_collection, "Topology")
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set_attribute(topology, "Dimensions", "0")
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set_attribute(topology, "Type", "NoTopology")
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grid = new_child(temporal_collection, "Grid")
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set_attribute(grid, "Name", "Grid")
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time = new_child(grid, "Time")
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set_attribute(time, "Value", "123")
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geometry = new_child(grid, "Geometry")
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set_attribute(geometry, "Type", "XYZ")
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dataitem = new_child(geometry, "DataItem")
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set_attribute(dataitem, "DataType", "Float")
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set_attribute(dataitem, "Dimensions", "12")
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", "4")
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add_text(dataitem, "0 0 0 1 0 0 0 1 0 0 0 1")
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topology = new_child(grid, "Topology")
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set_attribute(topology, "Dimensions", "1")
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set_attribute(topology, "Type", "Mixed")
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dataitem = new_child(topology, "DataItem")
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set_attribute(dataitem, "DataType", "Int")
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set_attribute(dataitem, "Dimensions", "5")
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 4)
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add_text(dataitem, "6 0 1 2 3")
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attribute = new_child(grid, "Attribute")
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set_attribute(attribute, "Center", "Cell")
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set_attribute(attribute, "Name", "Temperature field")
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set_attribute(attribute, "Type", "Scalar")
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dataitem = new_child(attribute, "DataItem")
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set_attribute(dataitem, "DataType", "Int")
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set_attribute(dataitem, "Dimensions", 1)
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 4)
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add_text(dataitem, "56")
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attribute = new_child(grid, "Attribute")
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set_attribute(attribute, "Center", "Node")
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set_attribute(attribute, "Name", "Density")
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set_attribute(attribute, "Type", "Vector")
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dataitem = new_child(attribute, "DataItem")
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set_attribute(dataitem, "DataType", "Float")
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set_attribute(dataitem, "Dimensions", 12)
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set_attribute(dataitem, "Format", "XML")
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set_attribute(dataitem, "Precision", 4)
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add_text(dataitem, "1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0")
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#save_file(xdoc, "/tmp/model.xmf")
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@fact string(xdoc) => testdata
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elements = [
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(:Tet10, [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
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(:Tet10, [11, 12, 13, 14, 15, 16, 17, 18, 19, 20])]
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displacement_field = nodes # same structure
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xdoc, model = JuliaFEM.Postprocess.xdmf_new_model()
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temporal_collection = JuliaFEM.Postprocess.xdmf_new_temporal_collection(model)
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grid = JuliaFEM.Postprocess.xdmf_new_grid(temporal_collection; time=1)
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JuliaFEM.Postprocess.xdmf_new_mesh!(grid, nodes, elements)
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JuliaFEM.Postprocess.xdmf_new_nodal_field!(grid, "Displacement", displacement_field)
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JuliaFEM.Postprocess.xdmf_save_model(xdoc, "/tmp/foo.xmf")
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#info("exported data model: \n$(string(xdoc))")
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#@test string(xdoc) == testdata
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d1 = split(string(xdoc), "\n")
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# d2 = split(testdata, "\n")
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d2 = open(readlines, Pkg.dir("JuliaFEM")*"/test/testdata/quad_two_tet10.xmf")
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println("comparing string")
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for i in 1:length(d1)
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println("d1: $(d1[i])")
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println("d2: $(d2[i])")
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#status = d1 == d2 ? "MATCHES" : "NO MATCH"
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#info("line: $(d1[i]) $status")
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#if d1 != d2
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# info("should be:\n$(d2[i])")
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#end
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d1 == d2 || error("No match")
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end
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end
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using JuliaFEM: xdmf_new_model, xdmf_new_grid, xdmf_new_temporal_collection, xdmf_new_mesh, xdmf_new_field, xdmf_save_model
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facts("test model write XML") do
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X = [0 0 0; 1 0 0; 0 1 0; 0 0 1]'
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elmap = [6 1 2 3 4]' # element type 6, nodes 1 2 3 4
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temperature_field = [56]
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density_field = Float64[1 2 3; 4 5 6; 7 8 9; 10 11 12]'
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xdoc, model = xdmf_new_model()
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temporal_collection = xdmf_new_temporal_collection(model)
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grid = xdmf_new_grid(temporal_collection; time=123)
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xdmf_new_mesh(grid, X, elmap)
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xdmf_new_field(grid, "Temperature field", "elements", temperature_field)
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xdmf_new_field(grid, "Density", "nodes", density_field)
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@fact string(xdoc) => testdata
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end
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facts("test that xdmf throws error when trying to add field not able to handle") do
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xdoc, model = xdmf_new_model()
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temporal_collection = xdmf_new_temporal_collection(model)
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grid = xdmf_new_grid(temporal_collection; time=123)
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temperature_field = ["56"] # strings not supported by xdmf
|
||||
@fact_throws xdmf_new_field(grid, "unknown field data", "elements", temperature_field)
|
||||
end
|
||||
|
||||
facts("test saving xdmf model") do
|
||||
xdoc, model = xdmf_new_model()
|
||||
# FIXME: xdoc here is just / of xml file, we're not interested of it but
|
||||
# xdmf_new_model returns it that we're able to save xml file.
|
||||
t = tempname()
|
||||
xdmf_save_model(xdoc, t)
|
||||
@fact isfile(t) => true
|
||||
end
|
||||
|
||||
Vendored
+52
-28
@@ -3,37 +3,61 @@
|
||||
<Domain>
|
||||
<Grid CollectionType="Temporal" GridType="Collection" Name="Collection">
|
||||
<Grid Name="Grid">
|
||||
<Time Value="1"/>
|
||||
<Geometry Type="XYZ">
|
||||
<Time Value="0"/>
|
||||
<DataItem DataType="Float" Dimensions="20 3" Format="XML" Precision="8">
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.5 0.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.5 0.0
|
||||
0.0 0.0 0.5
|
||||
0.5 0.0 0.5
|
||||
0.0 0.5 0.5
|
||||
1.0 1.0 1.0
|
||||
2.0 1.0 1.0
|
||||
1.0 2.0 1.0
|
||||
1.0 1.0 2.0
|
||||
1.5 1.0 1.0
|
||||
1.5 1.5 1.0
|
||||
1.0 1.5 1.0
|
||||
1.0 1.0 1.5
|
||||
1.5 1.0 1.5
|
||||
1.0 1.5 1.5
|
||||
</DataItem>
|
||||
<DataItem DataType="Float" Dimensions="60" Format="XML" Precision="8">
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.5 0.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.5 0.0
|
||||
0.0 0.0 0.5
|
||||
0.5 0.0 0.5
|
||||
0.0 0.5 0.5
|
||||
1.0 1.0 1.0
|
||||
2.0 1.0 1.0
|
||||
1.0 2.0 1.0
|
||||
1.0 1.0 2.0
|
||||
1.5 1.0 1.0
|
||||
1.5 1.5 1.0
|
||||
1.0 1.5 1.0
|
||||
1.0 1.0 1.5
|
||||
1.5 1.0 1.5
|
||||
1.0 1.5 1.5
|
||||
</DataItem>
|
||||
</Geometry>
|
||||
<Topology TopologyType="Mixed" NumberOfElements="2" >
|
||||
<DataItem Format="XML" DataType="Int" Dimensions="2 11">
|
||||
38 0 1 2 3 4 5 6 7 8 9
|
||||
38 10 11 12 13 14 15 16 17 18 19
|
||||
</DataItem>
|
||||
<Topology TopologyType="Mixed" NumberOfElements="2">
|
||||
<DataItem Format="XML" DataType="Int" Dimensions="22">
|
||||
38 0 1 2 3 4 5 6 7 8 9
|
||||
38 10 11 12 13 14 15 16 17 18 19
|
||||
</DataItem>
|
||||
</Topology>
|
||||
<Attribute Center="Node" Name="Displacement" Type="Vector">
|
||||
<DataItem DataType="Float" Dimensions="60" Format="XML" Precision="8">
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.5 0.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.5 0.0
|
||||
0.0 0.0 0.5
|
||||
0.5 0.0 0.5
|
||||
0.0 0.5 0.5
|
||||
1.0 1.0 1.0
|
||||
2.0 1.0 1.0
|
||||
1.0 2.0 1.0
|
||||
1.0 1.0 2.0
|
||||
1.5 1.0 1.0
|
||||
1.5 1.5 1.0
|
||||
1.0 1.5 1.0
|
||||
1.0 1.0 1.5
|
||||
1.5 1.0 1.5
|
||||
1.0 1.5 1.5
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
</Grid>
|
||||
</Grid>
|
||||
</Domain>
|
||||
|
||||
Reference in New Issue
Block a user