Add ExtendableFEM.jl benchmark implementation

benchmarks/linear-elastic-plate-with-hole/extendablefem/Project.toml

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+[deps]
+ExtendableFEM = "a722555e-65e0-4074-a036-ca7ce79a4aed"
+ExtendableGrids = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
+Fire = "652a1917-b8e5-5d9b-be38-bbf27e56fe44"
+Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
+GridVisualize = "5eed8a63-0fb0-45eb-886d-8d5a387d12b8"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+ZipArchives = "49080126-0e18-4c2a-b176-c102e4b3760c"
+
+[compat]
+LinearSolve = "~3.50.0"

benchmarks/linear-elastic-plate-with-hole/extendablefem/Snakefile

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+
+import json
+import os
+
+tool = "extendablefem"
+result_dir = "snakemake_results/" + config["benchmark"] 
+configuration_to_parameter_file = config["configuration_to_parameter_file"]
+configurations = config["configurations"]
+
+rule setup_julia_environment:
+    input: f"{tool}/Project.toml"
+    output: manifest=f"{tool}/Manifest.toml"
+    singularity: "docker://julia:1.12.2-bookworm"
+    shell: 
+        """
+        julia --project={tool} -e 'using Pkg;Pkg.instantiate()'
+        """
+
+rule run_extendablefem_simulation:
+    input: 
+        parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
+        mesh = f"{result_dir}/mesh/mesh_{{configuration}}.msh",
+        manifest = f"{tool}/Manifest.toml",
+    output:
+        zip = f"{result_dir}/{{tool}}/solution_field_data_{{configuration}}.zip",
+        metrics = f"{result_dir}/{{tool}}/solution_metrics_{{configuration}}.json",
+    singularity: "docker://julia:1.12.2-bookworm"
+    shell:
+        """
+        julia --project={tool} {tool}/run_extendablefem_simulation.jl --configfile {input.parameters} --meshfile {input.mesh} --outputzip {output.zip} --outputmetrics {output.metrics}
+        """
+

benchmarks/linear-elastic-plate-with-hole/extendablefem/run_extendablefem_simulation.jl

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+using JSON
+using Fire
+using Gmsh
+using ExtendableGrids
+using ExtendableFEM
+using StaticArrays: @SArray
+using Unitful
+using LinearAlgebra
+using ZipArchives: ZipWriter, zip_newfile
+
+struct PlateConfig
+    id::String
+    F::Float64
+    E::Float64
+    ν::Float64
+    radius::Float64
+    length::Float64
+    element_order::Int64
+end
+
+struct Metrics
+    max_von_mises_stress_nodes::Float64
+end
+
+function value_with_unit(json::JSON.Object{String,Any})
+    res = uparse(string(json["value"])*json["unit"])
+    return res
+end
+
+
+function parse_config(configfile::String)
+    config = JSON.parsefile(configfile)
+    id =  config["configuration"]
+    F = ustrip(u"Pa",value_with_unit(config["load"]))
+    E = ustrip(u"Pa",value_with_unit(config["young-modulus"]))
+    ν = config["poisson-ratio"]["value"]
+    radius = ustrip(u"m",value_with_unit(config["radius"]))
+    length = ustrip(u"m",value_with_unit(config["length"]))
+    element_order = config["element-order"]
+    return PlateConfig(id,F,E,ν,radius,length,element_order)
+end
+
+
+function plane_stress_elasticity_tensor(E::Float64, ν::Float64)
+    G = (1 / (1 + ν)) * E * 0.5
+    λ = (ν / (1 - 2ν)) * 2 * G
+    return @SArray [
+        (λ + 2G) λ 0
+        λ (λ + 2G) 0
+        0 0 G
+    ]
+end
+
+
+function make_kernel(𝐂)
+    function LE_kernel_sym!(σ,εv,qpinfo)
+        mul!(σ,𝐂,εv)
+    end 
+    return LE_kernel_sym!
+end
+
+function u_ex_kernel!(result,qpinfo)
+    x = qpinfo.x[1]
+    y = qpinfo.x[2]
+    a = qpinfo.params[1]
+    T = qpinfo.params[2]
+    E = qpinfo.params[3]
+    ν = qpinfo.params[4]
+    r = sqrt(x^2+y^2)
+    θ = atan(y,x)
+    k = (3.0-ν)/(1.0+ν)
+    Ta_8mu = T*a*(1.0+ν)/(4.0*E)
+    ct = cos(θ)
+    c3t = cos(3.0*θ)
+    st = sin(θ)
+    s3t = sin(3.0*θ)
+    fac = 2.0 * (a/r)^3
+
+
+    result[1] = Ta_8mu * (
+          (r/a) * (k + 1.0) * ct
+        + 2.0*(a/r)*((1.0 + k) * ct + c3t)
+        - fac * c3t
+    )
+    result[2] = Ta_8mu * (
+          (r/a) * (k - 3.0) * st
+        + 2.0*(a/r)*((1.0 - k) * st + s3t)
+        - fac * s3t
+    )
+end
+
+function exact_error!(result,u, qpinfo)
+    u_ex_kernel!(result,qpinfo)
+    result .-= u 
+    result .= result .^2
+    return nothing
+end
+
+function solve_plate_with_hole(config::PlateConfig,grid::ExtendableGrid,outputzip::String,outputmetrics::String)
+
+    bfacemask!(grid,[0.,0.],[config.radius,config.radius],50)
+
+    PD = ProblemDescription("Linear elastic 2D Plate with hole, configuration "*config.id)
+    u = Unknown("u"; name= "displacement")
+    assign_unknown!(PD, u)
+    𝐂 = plane_stress_elasticity_tensor(config.E,config.ν)
+    LE_kernel_sym! = make_kernel(𝐂)
+    assign_operator!(PD, BilinearOperator(LE_kernel_sym!, [εV(u,1.0)]))
+    assign_operator!(PD, InterpolateBoundaryData(u, u_ex_kernel!; regions = [3,4], params = [config.radius,config.F,config.E,config.ν]))
+    assign_operator!(PD, HomogeneousBoundaryData(u; regions = [1], mask = [1,0]))
+    assign_operator!(PD, HomogeneousBoundaryData(u; regions = [2], mask = [0,1]))
+
+    FEType = H1Pk{2,2, config.element_order}
+    FES = FESpace{FEType}(grid)
+    sol = solve(PD,FES; timeroutputs = :hide)
+
+    u_ex = FEVector(FES; name="exact solution")
+    interpolate!(u_ex.FEVectorBlocks[1],ON_CELLS,u_ex_kernel!;params = [config.radius,config.F,config.E,config.ν])
+    u_exx = nodevalues(u_ex.FEVectorBlocks[1])[1,:]
+    u_exy = nodevalues(u_ex.FEVectorBlocks[1])[2,:]
+
+    u_x = nodevalues(sol[u])[1,:]
+    u_y = nodevalues(sol[u])[2,:]
+    u_mag = sqrt.(u_x.*u_x.+u_y.*u_y)
+    uex_mag = sqrt.(u_exx.*u_exx.+u_exy.*u_exy)
+
+    # TODO: Stress calculations
+
+    metrics = Metrics(0.)
+    # TODO: L2 error, see Example301
+    ErrorIntegrationExact = ItemIntegrator(exact_error!, [id(u)]; quadorder = 8,params = [config.radius,config.F,config.E,config.ν])
+
+    error = evaluate(ErrorIntegrationExact, sol)
+
+    L2error = sqrt(sum(error))
+
+    outputvtk = splitdir(outputzip)[1]*"/results_"*config.id*".vtu";
+    writeVTK(outputvtk,grid;compress=false, u_x=u_x,u_y=u_y,u_mag=u_mag,uexx=u_exx,uexy=u_exy,uex=uex_mag)
+    f = open(outputvtk,"r")
+    vtkcontent = read(f,String)
+    ZipWriter(outputzip) do w
+        zip_newfile(w, "result_"*config.id*".vtu";compress=true)
+        write(w,vtkcontent)
+    end
+    JSON.json(outputmetrics,metrics;pretty=true)
+
+end
+
+"run linear elastic plate with a hole using ExtendableFEM.jl"
+Fire.@main function run_simulation(;
+    configfile::String="", 
+    meshfile::String="",
+    outputzip::String="",
+    outputmetrics::String=""
+)
+    if(isempty(configfile))
+        @error "No configuration file given"
+    end
+    config = parse_config(configfile)
+    if(isempty(meshfile))
+        @error "No mesh file given"
+    end
+    if(isempty(outputzip))
+        @error "No output zip file given"
+    end
+    if(isempty(outputmetrics))
+        @error "No output metrics file given"
+    end
+    grid = simplexgrid_from_gmsh(meshfile)
+    solve_plate_with_hole(config,grid,outputzip,outputmetrics)
+
+    return
+end