diff --git a/src/xdmf.jl b/src/xdmf.jl index c117a63..4f87610 100644 --- a/src/xdmf.jl +++ b/src/xdmf.jl @@ -35,20 +35,12 @@ using LightXML # > #define XDMF_3DSMESH 0x1100 # > #define XDMF_3DRECTMESH 0x1101 # > #define XDMF_3DCORECTMESH 0x1102 -""" -Build a new model for outout -Parameters ----------- +global eltypes = Dict{Symbol, Int}( + :Tet4 => 0x6, + :Quad4 => 0x5, + :Tet10 => 0x0026) -Examples -------- - -```julia -@assert 1+1 == 3 -``` - -""" function xdmf_new_model(xdmf_version="2.1") xdoc = XMLDocument() xroot = create_root(xdoc, "Xdmf") @@ -63,11 +55,11 @@ function xdmf_new_temporal_collection(model) set_attribute(temporal_collection, "CollectionType", "Temporal") set_attribute(temporal_collection, "GridType", "Collection") set_attribute(temporal_collection, "Name", "Collection") - geometry = new_child(temporal_collection, "Geometry") - set_attribute(geometry, "Type", "None") - topology = new_child(temporal_collection, "Topology") - set_attribute(topology, "Dimensions", "0") - set_attribute(topology, "Type", "NoTopology") +# geometry = new_child(temporal_collection, "Geometry") +# set_attribute(geometry, "Type", "None") +# topology = new_child(temporal_collection, "Topology") +# set_attribute(topology, "Dimensions", "0") +# set_attribute(topology, "Type", "NoTopology") return temporal_collection end @@ -79,102 +71,51 @@ function xdmf_new_grid(temporal_collection; time=0) return grid end -#function xdmf_new_mesh(grid, X, elmap) -# geometry = new_child(grid, "Geometry") -# set_attribute(geometry, "Type", "XYZ") -# dataitem = new_child(geometry, "DataItem") -# set_attribute(dataitem, "DataType", "Float") -# set_attribute(dataitem, "Dimensions", length(X)) -# set_attribute(dataitem, "Format", "XML") -# set_attribute(dataitem, "Precision", "4") -# add_text(dataitem, join(X, " ")) -# topology = new_child(grid, "Topology") -# set_attribute(topology, "Dimensions", "1") -# set_attribute(topology, "Type", "Mixed") -# dataitem = new_child(topology, "DataItem") -# set_attribute(dataitem, "DataType", "Int") -# set_attribute(dataitem, "Dimensions", length(elmap)) -# set_attribute(dataitem, "Format", "XML") -# set_attribute(dataitem, "Precision", 4) -# elmap2 = copy(elmap) -# elmap2[2:end,:] -= 1 -# add_text(dataitem, join(elmap2, " ")) -#end +function xdmf_new_mesh!(grid, nodes, elements) -function xdmf_new_mesh(grid, X, elmap) - dim, nnodes = size(X) + # 1. write nodes geometry = new_child(grid, "Geometry") set_attribute(geometry, "Type", "XYZ") dataitem = new_child(geometry, "DataItem") set_attribute(dataitem, "DataType", "Float") - set_attribute(dataitem, "Dimensions", "$nnodes $dim") + ndim = sum([length(node) for node in nodes]) + info("XDFM: ndim = $ndim") + set_attribute(dataitem, "Dimensions", "$ndim") set_attribute(dataitem, "Format", "XML") set_attribute(dataitem, "Precision", 8) - #add_text(dataitem, join(X, " ")) - s = "\n" - - for i=1:nnodes - s *= "\t\t" * join(X[:,i], " ") * "\n" - end - s *= " " - add_text(dataitem, s) - - elmap2 = copy(elmap) - elmap2[2:end,:] -= 1 - dim, nelements = size(elmap2) + s = join([join(node, " ") for node in round(nodes, 5)], "\n") + add_text(dataitem, "\n"*s*"\n") + # 2. write elements topology = new_child(grid, "Topology") - #set_attribute(topology, "Dimensions", "1") + eldim = sum([length(element[2]) for element in elements]) + length(elements) set_attribute(topology, "TopologyType", "Mixed") - set_attribute(topology, "NumberOfElements", nelements) + set_attribute(topology, "NumberOfElements", length(elements)) dataitem = new_child(topology, "DataItem") - set_attribute(dataitem, "DataType", "Int") - set_attribute(dataitem, "Dimensions", "$nelements $dim") set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", 8) - s = "\n" - for i=1:nelements - s *= "\t\t" * join(elmap2[:,i], " ") * "\n" - end - add_text(dataitem, s) - #add_text(dataitem, join(elmap2, " ")) + set_attribute(dataitem, "DataType", "Int") + set_attribute(dataitem, "Dimensions", "$eldim") +# set_attribute(dataitem, "Precision", 8) + # note: id numbers start from 0 in Xdmf + s = join([join([eltypes[eltype]; connectivity-1], " ") for (eltype, connectivity) in elements], "\n") + add_text(dataitem, "\n"*s*"\n") + end - -function xdmf_new_field(grid, name, source, data) - loc = Dict("elements" => "Cell", - "nodes" => "Node") - - dim1, dim2 = size(data'') - if dim1 == 1 - Type = "Scalar" - end - if dim1 == 3 - Type = "Vector" - end - - typ = string(typeof(data)) - datatype = "unknown" - for j in ["Int", "Float"] - if contains(typ, j) - datatype = j - end - end - if datatype == "unknown" - throw("unknown data type ", typ) - end - - +""" Write Vector field to nodes. """ +function xdmf_new_nodal_field!(grid, name, data) attribute = new_child(grid, "Attribute") - set_attribute(attribute, "Center", loc[source]) + set_attribute(attribute, "Center", "Node") set_attribute(attribute, "Name", name) - set_attribute(attribute, "Type", Type) + set_attribute(attribute, "Type", "Vector") dataitem = new_child(attribute, "DataItem") - set_attribute(dataitem, "DataType", datatype) - set_attribute(dataitem, "Dimensions", length(data)) + set_attribute(dataitem, "DataType", "Float") + ndim = sum([length(d) for d in data]) + set_attribute(dataitem, "Dimensions", "$ndim") set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", 4) - add_text(dataitem, join(data, " ")) + set_attribute(dataitem, "Precision", 8) + s = join([join(d, " ") for d in round(data, 5)], "\n") + add_text(dataitem, "\n"*s*"\n") end function xdmf_save_model(xdoc, filename) diff --git a/test/test_xdmf.jl b/test/test_xdmf.jl index 8c4f922..559ce30 100644 --- a/test/test_xdmf.jl +++ b/test/test_xdmf.jl @@ -1,32 +1,72 @@ # 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) +module XDMFTests -using LightXML +using JuliaFEM +using JuliaFEM.Postprocess +using JuliaFEM.Test testdata = """\ - - - @@ -34,100 +74,56 @@ testdata = """\ """ -# makes no sense for vector field -# 1 2 4 7 +function test_write_to_xml() + nodes = Vector{Float64}[ + [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]] -facts("test test data") do - xdoc = XMLDocument() - xroot = create_root(xdoc, "Xdmf") - set_attribute(xroot, "xmlns:xi", "http://www.w3.org/2001/XInclude") - set_attribute(xroot, "Version", "2.1") - domain = new_child(xroot, "Domain") - temporal_collection = new_child(domain, "Grid") - set_attribute(temporal_collection, "CollectionType", "Temporal") - set_attribute(temporal_collection, "GridType", "Collection") - set_attribute(temporal_collection, "Name", "Collection") - geometry = new_child(temporal_collection, "Geometry") - set_attribute(geometry, "Type", "None") - topology = new_child(temporal_collection, "Topology") - set_attribute(topology, "Dimensions", "0") - set_attribute(topology, "Type", "NoTopology") - - grid = new_child(temporal_collection, "Grid") - set_attribute(grid, "Name", "Grid") - time = new_child(grid, "Time") - set_attribute(time, "Value", "123") - geometry = new_child(grid, "Geometry") - set_attribute(geometry, "Type", "XYZ") - dataitem = new_child(geometry, "DataItem") - set_attribute(dataitem, "DataType", "Float") - set_attribute(dataitem, "Dimensions", "12") - set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", "4") - add_text(dataitem, "0 0 0 1 0 0 0 1 0 0 0 1") - - topology = new_child(grid, "Topology") - set_attribute(topology, "Dimensions", "1") - set_attribute(topology, "Type", "Mixed") - dataitem = new_child(topology, "DataItem") - set_attribute(dataitem, "DataType", "Int") - set_attribute(dataitem, "Dimensions", "5") - set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", 4) - add_text(dataitem, "6 0 1 2 3") - attribute = new_child(grid, "Attribute") - set_attribute(attribute, "Center", "Cell") - set_attribute(attribute, "Name", "Temperature field") - set_attribute(attribute, "Type", "Scalar") - dataitem = new_child(attribute, "DataItem") - set_attribute(dataitem, "DataType", "Int") - set_attribute(dataitem, "Dimensions", 1) - set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", 4) - add_text(dataitem, "56") - attribute = new_child(grid, "Attribute") - set_attribute(attribute, "Center", "Node") - set_attribute(attribute, "Name", "Density") - set_attribute(attribute, "Type", "Vector") - dataitem = new_child(attribute, "DataItem") - set_attribute(dataitem, "DataType", "Float") - set_attribute(dataitem, "Dimensions", 12) - set_attribute(dataitem, "Format", "XML") - set_attribute(dataitem, "Precision", 4) - 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") - #save_file(xdoc, "/tmp/model.xmf") - @fact string(xdoc) => testdata + elements = [ + (:Tet10, [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]) + (:Tet10, [11, 12, 13, 14, 15, 16, 17, 18, 19, 20])] + + displacement_field = nodes # same structure + xdoc, model = JuliaFEM.Postprocess.xdmf_new_model() + temporal_collection = JuliaFEM.Postprocess.xdmf_new_temporal_collection(model) + grid = JuliaFEM.Postprocess.xdmf_new_grid(temporal_collection; time=1) + JuliaFEM.Postprocess.xdmf_new_mesh!(grid, nodes, elements) + JuliaFEM.Postprocess.xdmf_new_nodal_field!(grid, "Displacement", displacement_field) + JuliaFEM.Postprocess.xdmf_save_model(xdoc, "/tmp/foo.xmf") + #info("exported data model: \n$(string(xdoc))") + #@test string(xdoc) == testdata + d1 = split(string(xdoc), "\n") +# d2 = split(testdata, "\n") + d2 = open(readlines, Pkg.dir("JuliaFEM")*"/test/testdata/quad_two_tet10.xmf") + println("comparing string") + for i in 1:length(d1) + println("d1: $(d1[i])") + println("d2: $(d2[i])") + #status = d1 == d2 ? "MATCHES" : "NO MATCH" + #info("line: $(d1[i]) $status") + #if d1 != d2 + # info("should be:\n$(d2[i])") + #end + d1 == d2 || error("No match") + end end -using JuliaFEM: xdmf_new_model, xdmf_new_grid, xdmf_new_temporal_collection, xdmf_new_mesh, xdmf_new_field, xdmf_save_model - -facts("test model write XML") do - X = [0 0 0; 1 0 0; 0 1 0; 0 0 1]' - elmap = [6 1 2 3 4]' # element type 6, nodes 1 2 3 4 - temperature_field = [56] - density_field = Float64[1 2 3; 4 5 6; 7 8 9; 10 11 12]' - xdoc, model = xdmf_new_model() - temporal_collection = xdmf_new_temporal_collection(model) - grid = xdmf_new_grid(temporal_collection; time=123) - xdmf_new_mesh(grid, X, elmap) - xdmf_new_field(grid, "Temperature field", "elements", temperature_field) - xdmf_new_field(grid, "Density", "nodes", density_field) - @fact string(xdoc) => testdata -end - -facts("test that xdmf throws error when trying to add field not able to handle") do - xdoc, model = xdmf_new_model() - temporal_collection = xdmf_new_temporal_collection(model) - grid = xdmf_new_grid(temporal_collection; time=123) - 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 diff --git a/test/testdata/quad_two_tet10.xmf b/test/testdata/quad_two_tet10.xmf index a831814..e534c40 100644 --- a/test/testdata/quad_two_tet10.xmf +++ b/test/testdata/quad_two_tet10.xmf @@ -3,37 +3,61 @@ +