Paraview catalyst #1

benegee · 2024-10-28T11:59:07Z

Created for discussion.
We will finally want to merge this to trixi-framework/Trixi.jl

…paraview-catalyst

…y works once implemented in paraviewcatalyst.jl)

…nt and catalyst callback

… of more mesh types

…ded data

…sier to run

…nterpolation

…t state (not working)

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 241 in 098e2bc

    
           x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) : vec(interpolation_node_coordinates[1, :, :, :, :])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 243 in 098e2bc

    
           y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) : vec(interpolation_node_coordinates[2, :, :, :, :])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 254 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 259 to 264 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([ 
        
               [(c_tr * gsy * gsx) + (c_y * gsx) + c_x 
        
               (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x 
        
               (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               (c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1] 
        
               for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 270 to 280 in 098e2bc

    
           connectivity = [0, 1, gsx + 1, gsx, gsy * gsx, gsy * gsx + 1, gsy * gsx + gsx + 1, gsy * gsx + gsx] 
        
           for c_x in 0:(gsx - 2), c_y in 0:(gsy - 2), c_z in 0:(gsz - 2), c_tr in 0:(gstr - 1) 
        
               if !(c_x == 0 && c_y == 0 && c_z == 0 && c_tr == 0) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1) 
        
                   push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 282 to 283 in 098e2bc

    
           end 
        
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = connectivity

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 303 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(interpolated_data[:, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 305 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(interpolated_data[:, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 313 in 098e2bc

    
           function create_conduit_node_no_interpolation(integrator, mesh::TreeMesh, equations, solver, cache)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 315 in 098e2bc

node = ParaViewCatalyst.ConduitNode()

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 325 in 098e2bc

    
           unstructured_data = get_unstructured_data(Trixi.wrap_array(integrator.u, integrator.p), solution_variables_, mesh, equations, solver, cache)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 327 to 333 in 098e2bc

    
           reshaped_data = (ndims(mesh) == 3) ? reshape(vcat([ 
        
               unstructured_data[i,j,k,l,m] 
        
               for m in 1:uds[5] for k in uds[3] for j in 1:uds[2] for l in 1:uds[4] for i in 1:uds[1] 
        
           ]...), :) : reshape(vcat([ 
        
               unstructured_data[i,j,k,l] 
        
               for l in 1:uds[4] for j in 1:uds[2] for k in 1:uds[3] for i in 1:uds[1] 
        
           ]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 345 in 098e2bc

    
           zs = (ndims(mesh) == 3) ? collect(range(-1, 1, length = resolution + 1)) .* length_level_0 / 2 .+

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 351 in 098e2bc

gsz =(ndims(mesh) == 3) ? size(zs)[1] : nothing

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 376 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims(mesh) == 2) ? "quad" : "hex"

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 381 to 386 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([ 
        
               [(c_y * gsx) + c_x 
        
               ((c_y + 1) * gsx) + c_x 
        
               ((c_y + 1) * gsx) + c_x + 1 
        
               (c_y * gsx) + c_x + 1] 
        
               for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2)]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 392 to 401 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([ 
        
               [(c_z * gsy * gsx) + (c_y * gsx) + c_x 
        
               (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1 
        
               (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x 
        
               ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x 
        
               ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1 
        
               ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x] 
        
               for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2)]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 412 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 416 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, :, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 420 in 098e2bc

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 424 in 098e2bc

    
           function create_conduit_node_no_interpolation(integrator, mesh::P4estMesh, equations, solver, cache)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 436 in 098e2bc

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 441 in 098e2bc

    
           unstructured_data = get_unstructured_data(Trixi.wrap_array(integrator.u, integrator.p), solution_variables_, mesh, equations, solver, cache)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 448 to 449 in 098e2bc

    
           gsz =(ndims_ == 3) ? grid_size[4] : nothing 
        
           gstr =(ndims_ == 3) ? grid_size[5] : grid_size[4]

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 456 in 098e2bc

    
           x = (ndims_ == 2) ? vec(node_coordinates[1, :, :, :]) : vec(node_coordinates[1, :, :, :, :])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 458 in 098e2bc

    
           y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) : vec(node_coordinates[2, :, :, :, :])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 469 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 474 to 479 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([ 
        
               [(c_tr * gsy * gsx) + (c_y * gsx) + c_x 
        
               (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x 
        
               (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               (c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1] 
        
               for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 485 to 494 in 098e2bc

    
           node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([ 
        
               [(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x 
        
               (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1 
        
               (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x 
        
               (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x 
        
               (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1 
        
               (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1 
        
               (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x] 
        
               for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2) for c_tr in 0:(gstr - 1)]...), :)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 504 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 506 in 098e2bc

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, :, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 524 to 526 in 098e2bc

    
           node = (visualization_callback.interpolation ?  
        
           create_conduit_node(integrator, mesh, equations, solver, cache, visualization_callback.nvisnodes) :  
        
           create_conduit_node_no_interpolation(integrator, mesh, equations, solver, cache))

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 552 in 098e2bc

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 554 to 566 in 098e2bc

    
           # Create output data structure 
        
           data_vis = Array{Float64}(undef, n_nodes_out, n_nodes_out, n_elements, n_variables) 
        
           # For each variable, interpolate element data and store to global data structure 
        
           for v in 1:n_variables 
        
             # Reshape data array for use in interpolate_nodes function 
        
             @views reshaped_data = reshape(data_gl[:, :, :, v], 1, n_nodes_in, n_nodes_in, n_elements) 
        
             # Interpolate data to visualization nodes 
        
             for element_id in 1:n_elements 
        
               @views data_vis[:, :, element_id, v] .= reshape( 
        
                   interpolate_nodes(reshaped_data[:, :, :, element_id], vandermonde, 1), 
        
                   n_nodes_out, n_nodes_out)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 568 in 098e2bc

end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 570 to 583 in 098e2bc

    
           # Create output data structure 
        
           data_vis = Array{Float64}(undef, n_nodes_out, n_nodes_out, n_nodes_out, n_elements, n_variables) 
        
           # For each variable, interpolate element data and store to global data structure 
        
           for v in 1:n_variables 
        
             # Reshape data array for use in interpolate_nodes function 
        
             @views reshaped_data = reshape(data_gl[:, :, :, :, v], 
        
                                            1, n_nodes_in, n_nodes_in, n_nodes_in, n_elements) 
        
             # Interpolate data to visualization nodes 
        
             for element_id in 1:n_elements 
        
               @views data_vis[:, :, :, element_id, v] .= reshape( 
        
                   interpolate_nodes(reshaped_data[:, :, :, :, element_id], vandermonde, 1), 
        
                   n_nodes_out, n_nodes_out, n_nodes_out)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 585 in 098e2bc

end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 587 in 098e2bc

error("Unsupported number of spatial dimensions: ", ndims_)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 589 in 098e2bc

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 596 in 098e2bc

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 603 in 098e2bc

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 605 in 098e2bc

n_nodes_in = size(vandermonde, 2)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 611 in 098e2bc

    
           acc += vandermonde[i, ii] * vandermonde[j, jj] * vandermonde[k, kk] * data_in[v, ii, jj, kk]

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 622 in 098e2bc

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 628 in 098e2bc

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 630 in 098e2bc

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 632 in 098e2bc

n_nodes_in = size(vandermonde, 2)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 640 in 098e2bc

acc += vandermonde[i, ii] * data_in[v, ii, jj] * vandermonde[j, jj]

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 650 in 098e2bc

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Trixi.jl/src/callbacks_step/visualization.jl

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           plot_data_creator 
        
           plot_creator 
        
           fig

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Trixi.jl/src/callbacks_step/visualization.jl

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Trixi.jl/src/callbacks_step/visualization.jl

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           if ndims(mesh) == 3 && visualization_callback.plot_data_creator == PlotData2D && visualization_callback.plot_creator == show_plot

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Trixi.jl/src/callbacks_step/visualization.jl

Line 137 in 098e2bc

    
           @trixi_timeit timer() "visualization initialize plot_data" plot_data = PlotData3D(u_ode, semi, solution_variables = solution_variables)

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Trixi.jl/src/callbacks_step/visualization.jl

Line 143 in 098e2bc

    
           @trixi_timeit timer() "visualization initialize volume" GLMakie.volume(visualization_callback.fig[intTo2DInt(v)...], plot_data.data[v], algorithm = :mip)

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Trixi.jl/src/callbacks_step/visualization.jl

Line 177 in 098e2bc

    
           @trixi_timeit timer() "visualization plot data" plot_data = plot_data_creator(u_ode, semi, solution_variables = solution_variables)

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 185 to 187 in 098e2bc

    
           @trixi_timeit timer() "visualization create plot" plot_creator(plot_data, variable_names; 
        
                        show_mesh = show_mesh, plot_arguments = plot_arguments, 
        
                        time = integrator.t, timestep = integrator.stats.naccept, fig = fig)

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 231 to 232 in 098e2bc

    
           cols = length(plots) 
        
           rows = 1

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Trixi.jl/src/callbacks_step/visualization.jl

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           cols = ceil(Int, sqrt(length(plots))) 
        
           rows = div(length(plots), cols, RoundUp)

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Trixi.jl/src/callbacks_step/visualization.jl

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return (1,1)

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Trixi.jl/src/callbacks_step/visualization.jl

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t = intTo2DInt(n-1)

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 264 to 265 in 098e2bc

    
           show_mesh = false, plot_arguments = Dict{Symbol, Any}(), 
        
           time = nothing, timestep = nothing, fig = nothing)

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Trixi.jl/src/visualization/recipes_plots.jl

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Trixi.jl/src/visualization/utilities.jl

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           levels, 
        
           length_level_0)

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Trixi.jl/src/visualization/utilities.jl

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           function element2index3D(normalized_coordinates, levels, resolution, nvisnodes_per_level)

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Trixi.jl/src/visualization/utilities.jl

Lines 1478 to 1483 in 098e2bc

    
           lower_left_front_coordinate[1, element_id] = (normalized_coordinates[1, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx) 
        
           lower_left_front_coordinate[2, element_id] = (normalized_coordinates[2, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx) 
        
           lower_left_front_coordinate[3, element_id] = (normalized_coordinates[3, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx)

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Trixi.jl/src/visualization/utilities.jl

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lt = (x, y) -> x .< y .- dx / 2)

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Trixi.jl/src/visualization/utilities.jl

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                                       lt = (x, y) -> x .< y .- dx / 2) 
        
           return transpose(hcat(id_x, id_y,id_z))

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Trixi.jl/src/visualization/utilities.jl

Line 1619 in 098e2bc

@assert size(node_coordinates, 1) == 3 "only works in 3D"

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Trixi.jl/src/visualization/utilities.jl

Lines 1625 to 1626 in 098e2bc

    
           (cells_per_dimension[1] + 1) * (cells_per_dimension[3] + 1) +  # y-direction 
        
           (cells_per_dimension[1] + 1) * (cells_per_dimension[2] + 1))    # z-direction

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Trixi.jl/src/visualization/utilities.jl

Lines 1649 to 1651 in 098e2bc

    
           x[i, line_index] = node_coordinates[1, end, 1, linear_indices[end, cell_y, cell_z]] 
        
           y[i, line_index] = node_coordinates[2, end, 1, linear_indices[end, cell_y, cell_z]] 
        
           z[i, line_index] = node_coordinates[3, end, 1, linear_indices[end, cell_y, cell_z]]

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Trixi.jl/src/visualization/utilities.jl

Lines 1668 to 1670 in 098e2bc

    
           x[i, line_index] = node_coordinates[1, 1, end, linear_indices[cell_x, end, cell_z]] 
        
           y[i, line_index] = node_coordinates[2, 1, end, linear_indices[cell_x, end, cell_z]] 
        
           z[i, line_index] = node_coordinates[3, 1, end, linear_indices[cell_x, end, cell_z]]

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Trixi.jl/src/visualization/utilities.jl

Lines 1687 to 1689 in 098e2bc

    
           x[i, line_index] = node_coordinates[1, 1, end, linear_indices[cell_x, cell_y, end]] 
        
           y[i, line_index] = node_coordinates[2, 1, end, linear_indices[cell_x, cell_y, end]] 
        
           z[i, line_index] = node_coordinates[3, 1, end, linear_indices[cell_x, cell_y, end]]

github-actions · 2024-12-13T12:41:47Z

examples/p4est_2d_dgsem/elixir_advection_basic_catalyst.jl

+# The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
+stepsize_callback = StepsizeCallback(cfl = 1.6)
+
+catalyst_callback = ParaViewCatalystCallback(interval=100)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

catalyst_callback = ParaViewCatalystCallback(interval=100)

catalyst_callback = ParaViewCatalystCallback(interval = 100)

github-actions · 2024-12-13T12:41:47Z

examples/p4est_3d_dgsem/elixir_advection_cubed_sphere_catalyst.jl

+# The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
+stepsize_callback = StepsizeCallback(cfl = 1.2)
+
+catalyst_callback = ParaViewCatalystCallback(interval=100, interpolation=true)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

catalyst_callback = ParaViewCatalystCallback(interval=100, interpolation=true)

catalyst_callback = ParaViewCatalystCallback(interval = 100, interpolation = true)

github-actions · 2024-12-13T12:41:47Z

examples/p4est_3d_dgsem/elixir_euler_circular_wind_nonconforming_catalyst.jl

+    rho = 1.0 + 0.1  * exp(-50 * ((lambda-1.0)^2/2.0 + (phi-0.4)^2)) +
+                0.08 * exp(-100 * ((lambda-0.8)^2/4.0 + (phi-0.5)^2))


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

rho = 1.0 + 0.1 * exp(-50 * ((lambda-1.0)^2/2.0 + (phi-0.4)^2)) +

0.08 * exp(-100 * ((lambda-0.8)^2/4.0 + (phi-0.5)^2))

rho = 1.0 + 0.1 * exp(-50 * ((lambda - 1.0)^2 / 2.0 + (phi - 0.4)^2)) +

0.08 * exp(-100 * ((lambda - 0.8)^2 / 4.0 + (phi - 0.5)^2))

github-actions · 2024-12-13T12:41:47Z

examples/p4est_3d_dgsem/elixir_euler_circular_wind_nonconforming_catalyst.jl

+                           adapt_initial_condition = true,
+                           adapt_initial_condition_only_refine = true)
+
+catalyst_callback = ParaViewCatalystCallback(interval=100)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

catalyst_callback = ParaViewCatalystCallback(interval=100)

catalyst_callback = ParaViewCatalystCallback(interval = 100)

github-actions · 2024-12-13T12:41:48Z

examples/p4est_3d_dgsem/elixir_euler_circular_wind_nonconforming_catalyst.jl

+# Enable threading of the RK method for better performance on multiple threads
+sol = solve(ode, RDPK3SpFSAL49(thread = OrdinaryDiffEq.True()); abstol = 1.0e-6,
+            reltol = 1.0e-6,
+            ode_default_options()..., callback = callbacks, maxiters=1e7);


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

ode_default_options()..., callback = callbacks, maxiters=1e7);

ode_default_options()..., callback = callbacks, maxiters = 1e7);

github-actions · 2024-12-13T12:41:50Z

src/callbacks_step/paraview_catalyst.jl

+            end
+        end
+    end
+


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Suggested change

github-actions · 2024-12-13T12:41:50Z

src/callbacks_step/paraview_catalyst.jl

+    return node
+end
+
+function create_conduit_node(integrator, mesh::P4estMesh, equations, solver, cache, nvisnodes)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

function create_conduit_node(integrator, mesh::P4estMesh, equations, solver, cache, nvisnodes)

function create_conduit_node(integrator, mesh::P4estMesh, equations, solver, cache,

nvisnodes)

github-actions · 2024-12-13T12:41:50Z

src/callbacks_step/paraview_catalyst.jl

+    varnames = Trixi.varnames(solution_variables_, equations)
+    timestep = integrator.stats.naccept
+
+


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Suggested change

github-actions · 2024-12-13T12:41:51Z

src/callbacks_step/paraview_catalyst.jl

+        nodes = collect(range(-1, 1, length=n_visnodes))
+        node_coordinates = Array{Float64, ndims_+2}(undef, ndims_, ntuple(_ -> n_visnodes, ndims_)..., Trixi.ncells(mesh))
+        interpolation_node_coordinates = calc_node_coordinates!(node_coordinates, mesh, nodes)
+        unstructured_data = get_unstructured_data(Trixi.wrap_array(integrator.u, integrator.p), solution_variables_, mesh, equations, solver, cache)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

nodes = collect(range(-1, 1, length=n_visnodes))

node_coordinates = Array{Float64, ndims_+2}(undef, ndims_, ntuple(_ -> n_visnodes, ndims_)..., Trixi.ncells(mesh))

interpolation_node_coordinates = calc_node_coordinates!(node_coordinates, mesh, nodes)

unstructured_data = get_unstructured_data(Trixi.wrap_array(integrator.u, integrator.p), solution_variables_, mesh, equations, solver, cache)

nodes = collect(range(-1, 1, length = n_visnodes))

node_coordinates = Array{Float64, ndims_ + 2}(undef, ndims_,

ntuple(_ -> n_visnodes,

ndims_)...,

Trixi.ncells(mesh))

interpolation_node_coordinates = calc_node_coordinates!(node_coordinates, mesh,

nodes)

unstructured_data = get_unstructured_data(Trixi.wrap_array(integrator.u,

integrator.p),

solution_variables_, mesh, equations,

solver, cache)

github-actions · 2024-12-13T12:41:51Z

src/callbacks_step/paraview_catalyst.jl

+    gsz =(ndims_ == 3) ? grid_size[4] : nothing
+    gstr =(ndims_ == 3) ? grid_size[5] : grid_size[4]


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

gsz =(ndims_ == 3) ? grid_size[4] : nothing

gstr =(ndims_ == 3) ? grid_size[5] : grid_size[4]

gsz = (ndims_ == 3) ? grid_size[4] : nothing

gstr = (ndims_ == 3) ? grid_size[5] : grid_size[4]

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 506 in 9b9e986

    
           node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, :, i])

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 524 to 526 in 9b9e986

    
           node = (visualization_callback.interpolation ?  
        
           create_conduit_node(integrator, mesh, equations, solver, cache, visualization_callback.nvisnodes) :  
        
           create_conduit_node_no_interpolation(integrator, mesh, equations, solver, cache))

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 533 in 9b9e986

end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 549 in 9b9e986

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 552 in 9b9e986

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 554 to 566 in 9b9e986

    
           # Create output data structure 
        
           data_vis = Array{Float64}(undef, n_nodes_out, n_nodes_out, n_elements, n_variables) 
        
           # For each variable, interpolate element data and store to global data structure 
        
           for v in 1:n_variables 
        
             # Reshape data array for use in interpolate_nodes function 
        
             @views reshaped_data = reshape(data_gl[:, :, :, v], 1, n_nodes_in, n_nodes_in, n_elements) 
        
             # Interpolate data to visualization nodes 
        
             for element_id in 1:n_elements 
        
               @views data_vis[:, :, element_id, v] .= reshape( 
        
                   interpolate_nodes(reshaped_data[:, :, :, element_id], vandermonde, 1), 
        
                   n_nodes_out, n_nodes_out)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 568 in 9b9e986

end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Lines 570 to 583 in 9b9e986

    
           # Create output data structure 
        
           data_vis = Array{Float64}(undef, n_nodes_out, n_nodes_out, n_nodes_out, n_elements, n_variables) 
        
           # For each variable, interpolate element data and store to global data structure 
        
           for v in 1:n_variables 
        
             # Reshape data array for use in interpolate_nodes function 
        
             @views reshaped_data = reshape(data_gl[:, :, :, :, v], 
        
                                            1, n_nodes_in, n_nodes_in, n_nodes_in, n_elements) 
        
             # Interpolate data to visualization nodes 
        
             for element_id in 1:n_elements 
        
               @views data_vis[:, :, :, element_id, v] .= reshape( 
        
                   interpolate_nodes(reshaped_data[:, :, :, :, element_id], vandermonde, 1), 
        
                   n_nodes_out, n_nodes_out, n_nodes_out)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 585 in 9b9e986

end

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 587 in 9b9e986

error("Unsupported number of spatial dimensions: ", ndims_)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 589 in 9b9e986

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 596 in 9b9e986

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 603 in 9b9e986

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 605 in 9b9e986

n_nodes_in = size(vandermonde, 2)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 611 in 9b9e986

    
           acc += vandermonde[i, ii] * vandermonde[j, jj] * vandermonde[k, kk] * data_in[v, ii, jj, kk]

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 622 in 9b9e986

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 628 in 9b9e986

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 630 in 9b9e986

vandermonde, n_vars) where T

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 632 in 9b9e986

n_nodes_in = size(vandermonde, 2)

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 640 in 9b9e986

acc += vandermonde[i, ii] * data_in[v, ii, jj] * vandermonde[j, jj]

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Trixi.jl/src/callbacks_step/paraview_catalyst.jl

Line 650 in 9b9e986

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 13 to 15 in 9b9e986

    
           plot_data_creator 
        
           plot_creator 
        
           fig

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Trixi.jl/src/callbacks_step/visualization.jl

Line 97 in 9b9e986

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/visualization.jl

Line 132 in 9b9e986

    
           if ndims(mesh) == 3 && visualization_callback.plot_data_creator == PlotData2D && visualization_callback.plot_creator == show_plot

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Trixi.jl/src/callbacks_step/visualization.jl

Line 137 in 9b9e986

    
           @trixi_timeit timer() "visualization initialize plot_data" plot_data = PlotData3D(u_ode, semi, solution_variables = solution_variables)

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Trixi.jl/src/callbacks_step/visualization.jl

Line 143 in 9b9e986

    
           @trixi_timeit timer() "visualization initialize volume" GLMakie.volume(visualization_callback.fig[intTo2DInt(v)...], plot_data.data[v], algorithm = :mip)

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/visualization.jl

Line 177 in 9b9e986

    
           @trixi_timeit timer() "visualization plot data" plot_data = plot_data_creator(u_ode, semi, solution_variables = solution_variables)

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 185 to 187 in 9b9e986

    
           @trixi_timeit timer() "visualization create plot" plot_creator(plot_data, variable_names; 
        
                        show_mesh = show_mesh, plot_arguments = plot_arguments, 
        
                        time = integrator.t, timestep = integrator.stats.naccept, fig = fig)

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/callbacks_step/visualization.jl

Lines 231 to 232 in 9b9e986

    
           cols = length(plots) 
        
           rows = 1

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 234 to 235 in 9b9e986

    
           cols = ceil(Int, sqrt(length(plots))) 
        
           rows = div(length(plots), cols, RoundUp)

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Trixi.jl/src/callbacks_step/visualization.jl

Line 251 in 9b9e986

return (1,1)

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Trixi.jl/src/callbacks_step/visualization.jl

Line 253 in 9b9e986

t = intTo2DInt(n-1)

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Trixi.jl/src/callbacks_step/visualization.jl

Lines 264 to 265 in 9b9e986

    
           show_mesh = false, plot_arguments = Dict{Symbol, Any}(), 
        
           time = nothing, timestep = nothing, fig = nothing)

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Trixi.jl/src/visualization/recipes_plots.jl

Lines 60 to 61 in 9b9e986

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Trixi.jl/src/visualization/utilities.jl

Lines 377 to 378 in 9b9e986

    
           levels, 
        
           length_level_0)

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Trixi.jl/src/visualization/utilities.jl

Line 1467 in 9b9e986

    
           function element2index3D(normalized_coordinates, levels, resolution, nvisnodes_per_level)

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Trixi.jl/src/visualization/utilities.jl

Lines 1478 to 1483 in 9b9e986

    
           lower_left_front_coordinate[1, element_id] = (normalized_coordinates[1, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx) 
        
           lower_left_front_coordinate[2, element_id] = (normalized_coordinates[2, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx) 
        
           lower_left_front_coordinate[3, element_id] = (normalized_coordinates[3, element_id] - 
        
                                                   (nvisnodes - 1) / 2 * dx)

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/visualization/utilities.jl

Line 1505 in 9b9e986

lt = (x, y) -> x .< y .- dx / 2)

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Trixi.jl/src/visualization/utilities.jl

Lines 1507 to 1508 in 9b9e986

    
                                       lt = (x, y) -> x .< y .- dx / 2) 
        
           return transpose(hcat(id_x, id_y,id_z))

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Trixi.jl/src/visualization/utilities.jl

Line 1619 in 9b9e986

@assert size(node_coordinates, 1) == 3 "only works in 3D"

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Trixi.jl/src/visualization/utilities.jl

Lines 1625 to 1626 in 9b9e986

    
           (cells_per_dimension[1] + 1) * (cells_per_dimension[3] + 1) +  # y-direction 
        
           (cells_per_dimension[1] + 1) * (cells_per_dimension[2] + 1))    # z-direction

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/visualization/utilities.jl

Lines 1649 to 1651 in 9b9e986

    
           x[i, line_index] = node_coordinates[1, end, 1, linear_indices[end, cell_y, cell_z]] 
        
           y[i, line_index] = node_coordinates[2, end, 1, linear_indices[end, cell_y, cell_z]] 
        
           z[i, line_index] = node_coordinates[3, end, 1, linear_indices[end, cell_y, cell_z]]

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/visualization/utilities.jl

Lines 1668 to 1670 in 9b9e986

    
           x[i, line_index] = node_coordinates[1, 1, end, linear_indices[cell_x, end, cell_z]] 
        
           y[i, line_index] = node_coordinates[2, 1, end, linear_indices[cell_x, end, cell_z]] 
        
           z[i, line_index] = node_coordinates[3, 1, end, linear_indices[cell_x, end, cell_z]]

[JuliaFormatter] _{reported by reviewdog 🐶}

Trixi.jl/src/visualization/utilities.jl

Lines 1687 to 1689 in 9b9e986

    
           x[i, line_index] = node_coordinates[1, 1, end, linear_indices[cell_x, cell_y, end]] 
        
           y[i, line_index] = node_coordinates[2, 1, end, linear_indices[cell_x, cell_y, end]] 
        
           z[i, line_index] = node_coordinates[3, 1, end, linear_indices[cell_x, cell_y, end]]

github-actions · 2024-12-13T12:47:19Z

src/callbacks_step/paraview_catalyst.jl

+    node["catalyst/state/time"] = timestep
+    node["catalyst/channels/input/type"] = "mesh"
+    node["catalyst/channels/input/data/coordsets/coords/type"] = "explicit"
+    x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) : vec(interpolation_node_coordinates[1, :, :, :, :])


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) : vec(interpolation_node_coordinates[1, :, :, :, :])

x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) :

vec(interpolation_node_coordinates[1, :, :, :, :])

github-actions · 2024-12-13T12:47:19Z

src/callbacks_step/paraview_catalyst.jl

+    node["catalyst/channels/input/data/coordsets/coords/type"] = "explicit"
+    x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) : vec(interpolation_node_coordinates[1, :, :, :, :])
+    node["catalyst/channels/input/data/coordsets/coords/values/x"] = x
+    y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) : vec(interpolation_node_coordinates[2, :, :, :, :])


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) : vec(interpolation_node_coordinates[2, :, :, :, :])

y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) :

vec(interpolation_node_coordinates[2, :, :, :, :])

github-actions · 2024-12-13T12:47:19Z

src/callbacks_step/paraview_catalyst.jl

+    #creating a topology
+    node["catalyst/channels/input/data/topologies/mesh/type"] = "unstructured"
+    node["catalyst/channels/input/data/topologies/mesh/coordset"] = "coords"
+    node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"

node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ?

"quad" : "hex"

github-actions · 2024-12-13T12:47:19Z

src/callbacks_step/paraview_catalyst.jl

+            node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
+                [(c_tr * gsy * gsx) + (c_y * gsx) + c_x
+                (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x
+                (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
+                (c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1]
+                for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([

[(c_tr * gsy * gsx) + (c_y * gsx) + c_x

(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x

(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1

(c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1]

for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([[(c_tr *

gsy *

gsx) +

(c_y *

gsx) +

c_x

(c_tr *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x

(c_tr *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x +

1

(c_tr *

gsy *

gsx) +

(c_y *

gsx) +

c_x +

1]

for c_x in 0:(gsx - 2)

for c_y in 0:(gsy - 2)

for c_tr in 0:(gstr - 1)]...),

:)

github-actions · 2024-12-13T12:47:19Z

src/callbacks_step/paraview_catalyst.jl

+        connectivity = [0, 1, gsx + 1, gsx, gsy * gsx, gsy * gsx + 1, gsy * gsx + gsx + 1, gsy * gsx + gsx]
+        for c_x in 0:(gsx - 2), c_y in 0:(gsy - 2), c_z in 0:(gsz - 2), c_tr in 0:(gstr - 1)
+            if !(c_x == 0 && c_y == 0 && c_z == 0 && c_tr == 0)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)
+                push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

connectivity = [0, 1, gsx + 1, gsx, gsy * gsx, gsy * gsx + 1, gsy * gsx + gsx + 1, gsy * gsx + gsx]

for c_x in 0:(gsx - 2), c_y in 0:(gsy - 2), c_z in 0:(gsz - 2), c_tr in 0:(gstr - 1)

if !(c_x == 0 && c_y == 0 && c_z == 0 && c_tr == 0)

push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x)

push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1)

push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)

push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x)

push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x)

push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1)

push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)

push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x)

connectivity = [

0,

1,

gsx + 1,

gsx,

gsy * gsx,

gsy * gsx + 1,

gsy * gsx + gsx + 1,

gsy * gsx + gsx

]

for c_x in 0:(gsx - 2), c_y in 0:(gsy - 2), c_z in 0:(gsz - 2),

c_tr in 0:(gstr - 1)

if !(c_x == 0 && c_y == 0 && c_z == 0 && c_tr == 0)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) +

c_x)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) +

c_x + 1)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) +

((c_y + 1) * gsx) + c_x + 1)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) +

((c_y + 1) * gsx) + c_x)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) +

(c_y * gsx) + c_x)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) +

(c_y * gsx) + c_x + 1)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) +

((c_y + 1) * gsx) + c_x + 1)

push!(connectivity,

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) +

((c_y + 1) * gsx) + c_x)

end

github-actions · 2024-12-13T12:47:21Z

src/callbacks_step/paraview_catalyst.jl

+    node["catalyst/channels/input/data/coordsets/coords/type"] = "explicit"
+    x = (ndims_ == 2) ? vec(node_coordinates[1, :, :, :]) : vec(node_coordinates[1, :, :, :, :])
+    node["catalyst/channels/input/data/coordsets/coords/values/x"] = x
+    y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) : vec(node_coordinates[2, :, :, :, :])


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) : vec(node_coordinates[2, :, :, :, :])

y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) :

vec(node_coordinates[2, :, :, :, :])

github-actions · 2024-12-13T12:47:22Z

src/callbacks_step/paraview_catalyst.jl

+    #creating a topology
+    node["catalyst/channels/input/data/topologies/mesh/type"] = "unstructured"
+    node["catalyst/channels/input/data/topologies/mesh/coordset"] = "coords"
+    node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"

node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ?

"quad" : "hex"

github-actions · 2024-12-13T12:47:22Z

src/callbacks_step/paraview_catalyst.jl

+            node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
+                [(c_tr * gsy * gsx) + (c_y * gsx) + c_x
+                (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x
+                (c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
+                (c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1]
+                for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([

[(c_tr * gsy * gsx) + (c_y * gsx) + c_x

(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x

(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1

(c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1]

for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([[(c_tr *

gsy *

gsx) +

(c_y *

gsx) +

c_x

(c_tr *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x

(c_tr *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x +

1

(c_tr *

gsy *

gsx) +

(c_y *

gsx) +

c_x +

1]

for c_x in 0:(gsx - 2)

for c_y in 0:(gsy - 2)

for c_tr in 0:(gstr - 1)]...),

:)

github-actions · 2024-12-13T12:47:22Z

src/callbacks_step/paraview_catalyst.jl

+            node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
+                [(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x
+                (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1
+                (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
+                (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x
+                (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x
+                (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1
+                (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
+                (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x]
+                for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2) for c_tr in 0:(gstr - 1)]...), :)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([

[(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1

(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1

(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x]

for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2) for c_tr in 0:(gstr - 1)]...), :)

node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([[(c_tr *

gsz *

gsy *

gsx) +

(c_z *

gsy *

gsx) +

(c_y *

gsx) +

c_x

(c_tr *

gsz *

gsy *

gsx) +

(c_z *

gsy *

gsx) +

(c_y *

gsx) +

c_x +

1

(c_tr *

gsz *

gsy *

gsx) +

(c_z *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x +

1

(c_tr *

gsz *

gsy *

gsx) +

(c_z *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x

(c_tr *

gsz *

gsy *

gsx) +

((c_z +

1) *

gsy *

gsx) +

(c_y *

gsx) +

c_x

(c_tr *

gsz *

gsy *

gsx) +

((c_z +

1) *

gsy *

gsx) +

(c_y *

gsx) +

c_x +

1

(c_tr *

gsz *

gsy *

gsx) +

((c_z +

1) *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x +

1

(c_tr *

gsz *

gsy *

gsx) +

((c_z +

1) *

gsy *

gsx) +

((c_y +

1) *

gsx) +

c_x]

for c_x in 0:(gsx - 2)

for c_y in 0:(gsy - 2)

for c_z in 0:(gsz - 2)

for c_tr in 0:(gstr - 1)]...),

:)

github-actions · 2024-12-13T12:47:22Z

src/callbacks_step/paraview_catalyst.jl

+        node["catalyst/channels/input/data/fields/" * varnames[i] * "/topology"] = "mesh"
+        node["catalyst/channels/input/data/fields/" * varnames[i] * "/volume_dependent"] = "false"
+        if ndims(mesh) == 2
+            node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, i])


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:, :, :, i])

node["catalyst/channels/input/data/fields/" * varnames[i] * "/values"] = vec(unstructured_data[:,

:,

:,

i])

benegee and others added 30 commits September 16, 2024 11:23

add ParaviewCatalystCallback skeleton

f80cb53

get package handling right

fbe8d1a

add example for data extraction

608346d

ParaviewCatalyst callback working except PlotData3D

6607023

Merge branch 'main' into paraview-catalyst

56fcd24

PlotData3D Skeleton

a69e8ce

some more restructuring

b38090b

cleanup

b153b92

missing end

1fef549

cleanup

2d68a94

fixed errors from merge

efc9c55

switch to PlotData3D

30028bb

fix type

b015842

add 3d interpolation

62f00c8

Merge branch 'paraview-catalyst' of github.com:benegee/Trixi.jl into …

d091643

…paraview-catalyst

PlotData3D working!

87d44f3

fixed catalyst for 1D and made 2D and 3D more efficient

e539ba5

removed path from initialize so it uses the environment variable (onl…

55322db

…y works once implemented in paraviewcatalyst.jl)

ein paar kommentare

1a36505

added example Linear Sclalar Advection 2D with Adaptive Mesh Refineme…

e59d36b

…nt and catalyst callback

support for custom paraview catalyst pipelines

f8bdb29

put the custom catalyst pipelines next to the corresponding examples

d88fbff

corrected a small mistake

ba0cdf4

making the paraview catalyst callback more modular for future support…

56e077a

… of more mesh types

paraview catalyst some preparations for p4estmesh

c86b248

small adjustments Trixi Paraview Catalyst p4estmesh

0aa23a7

some updates on paraview catalyst p4estmesh grid

06e0915

Paraview P4estMesh Working Mesh (interpolation not implemented yet)

1f73989

removed unneccessary code in paraview catalyst

312a4f4

Paraview Catalyst p4est current state - grid maybe working but hardco…

5340530

…ded data

s6nistam and others added 19 commits October 15, 2024 16:14

working paraview catalyst for p4estmesh supporting multiple variables

be8a1d1

paraview catalyst adjusted example to use less refinement so it is ea…

ce4dc3b

…sier to run

paraview catalyst some code cleanup and comments

5517231

paraview catalyst new example for testing

152fdf5

paraview catalyst docstring and some speed improvements

2d64105

Paraview Catalyst first idea for documentation

2156c59

Paraview Catalyst improvements to documentation

ab40318

paraview catalyst current state for visualizing efficiently without i…

d063be0

…nterpolation

paraview catalyst visualisation without interpolation treemesh curren…

16664cd

…t state (not working)

Paraview Catalyst Treemesh without interpolation current state

e8b5998

Paraview Catalyst 2x Memory save in p4estmesh connectivity array 3D

0d5a5bb

visualisation with plots 3D current state

5cfd42d

Plot3D without Paraview current state

8cf91f3

Visualization Callback 3D with Makie current state

27b8ba0

Visualization Callback working in 3D for TreeMeshes

eccf911

Visualization Callback with Makie now in just one window

4816143

Visualization Callback with Makie: refactored code

13d8ed0

visualisation callback new file for testing

246139e

renamed ParaviewCatalyst to ParaViewCatalyst

098e2bc

github-actions bot reviewed Dec 13, 2024

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fixed a typo in ParaViewCatalyst documentation

9b9e986

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Paraview catalyst #1

Paraview catalyst #1

benegee commented Oct 28, 2024

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	node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
	[(c_tr * gsy * gsx) + (c_y * gsx) + c_x
	(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x
	(c_tr * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
	(c_tr * gsy * gsx) + (c_y * gsx) + c_x + 1]
	for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_tr in 0:(gstr - 1)]...), :)

	connectivity = [0, 1, gsx + 1, gsx, gsy * gsx, gsy * gsx + 1, gsy * gsx + gsx + 1, gsy * gsx + gsx]
	for c_x in 0:(gsx - 2), c_y in 0:(gsy - 2), c_z in 0:(gsz - 2), c_tr in 0:(gstr - 1)
	if !(c_x == 0 && c_y == 0 && c_z == 0 && c_tr == 0)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1)
	push!(connectivity, (c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x)

	reshaped_data = (ndims(mesh) == 3) ? reshape(vcat([
	unstructured_data[i,j,k,l,m]
	for m in 1:uds[5] for k in uds[3] for j in 1:uds[2] for l in 1:uds[4] for i in 1:uds[1]
	]...), :) : reshape(vcat([
	unstructured_data[i,j,k,l]
	for l in 1:uds[4] for j in 1:uds[2] for k in 1:uds[3] for i in 1:uds[1]
	]...), :)

	node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
	[(c_y * gsx) + c_x
	((c_y + 1) * gsx) + c_x
	((c_y + 1) * gsx) + c_x + 1
	(c_y * gsx) + c_x + 1]
	for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2)]...), :)

	node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
	[(c_z * gsy * gsx) + (c_y * gsx) + c_x
	(c_z * gsy * gsx) + (c_y * gsx) + c_x + 1
	(c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
	(c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x
	((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x
	((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1
	((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
	((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x]
	for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2)]...), :)

	gsz =(ndims_ == 3) ? grid_size[4] : nothing
	gstr =(ndims_ == 3) ? grid_size[5] : grid_size[4]

	node["catalyst/channels/input/data/topologies/mesh/elements/connectivity"] = reshape(vcat([
	[(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x
	(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + (c_y * gsx) + c_x + 1
	(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
	(c_tr * gsz * gsy * gsx) + (c_z * gsy * gsx) + ((c_y + 1) * gsx) + c_x
	(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x
	(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + (c_y * gsx) + c_x + 1
	(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x + 1
	(c_tr * gsz * gsy * gsx) + ((c_z + 1) * gsy * gsx) + ((c_y + 1) * gsx) + c_x]
	for c_x in 0:(gsx - 2) for c_y in 0:(gsy - 2) for c_z in 0:(gsz - 2) for c_tr in 0:(gstr - 1)]...), :)

	node = (visualization_callback.interpolation ?
	create_conduit_node(integrator, mesh, equations, solver, cache, visualization_callback.nvisnodes) :
	create_conduit_node_no_interpolation(integrator, mesh, equations, solver, cache))

	# Create output data structure
	data_vis = Array{Float64}(undef, n_nodes_out, n_nodes_out, n_elements, n_variables)

	# For each variable, interpolate element data and store to global data structure
	for v in 1:n_variables
	# Reshape data array for use in interpolate_nodes function
	@views reshaped_data = reshape(data_gl[:, :, :, v], 1, n_nodes_in, n_nodes_in, n_elements)

	# Interpolate data to visualization nodes
	for element_id in 1:n_elements
	@views data_vis[:, :, element_id, v] .= reshape(
	interpolate_nodes(reshaped_data[:, :, :, element_id], vandermonde, 1),
	n_nodes_out, n_nodes_out)

	@trixi_timeit timer() "visualization create plot" plot_creator(plot_data, variable_names;
	show_mesh = show_mesh, plot_arguments = plot_arguments,
	time = integrator.t, timestep = integrator.stats.naccept, fig = fig)

	cols = ceil(Int, sqrt(length(plots)))
	rows = div(length(plots), cols, RoundUp)

	show_mesh = false, plot_arguments = Dict{Symbol, Any}(),
	time = nothing, timestep = nothing, fig = nothing)

	lower_left_front_coordinate[1, element_id] = (normalized_coordinates[1, element_id] -
	(nvisnodes - 1) / 2 * dx)
	lower_left_front_coordinate[2, element_id] = (normalized_coordinates[2, element_id] -
	(nvisnodes - 1) / 2 * dx)
	lower_left_front_coordinate[3, element_id] = (normalized_coordinates[3, element_id] -
	(nvisnodes - 1) / 2 * dx)

	lt = (x, y) -> x .< y .- dx / 2)
	return transpose(hcat(id_x, id_y,id_z))

	(cells_per_dimension[1] + 1) * (cells_per_dimension[3] + 1) + # y-direction
	(cells_per_dimension[1] + 1) * (cells_per_dimension[2] + 1)) # z-direction

	x[i, line_index] = node_coordinates[1, end, 1, linear_indices[end, cell_y, cell_z]]
	y[i, line_index] = node_coordinates[2, end, 1, linear_indices[end, cell_y, cell_z]]
	z[i, line_index] = node_coordinates[3, end, 1, linear_indices[end, cell_y, cell_z]]

	x[i, line_index] = node_coordinates[1, 1, end, linear_indices[cell_x, end, cell_z]]
	y[i, line_index] = node_coordinates[2, 1, end, linear_indices[cell_x, end, cell_z]]
	z[i, line_index] = node_coordinates[3, 1, end, linear_indices[cell_x, end, cell_z]]

	catalyst_callback = ParaViewCatalystCallback(interval=100)
	catalyst_callback = ParaViewCatalystCallback(interval = 100)

		rho = 1.0 + 0.1 * exp(-50 * ((lambda-1.0)^2/2.0 + (phi-0.4)^2)) +
		0.08 * exp(-100 * ((lambda-0.8)^2/4.0 + (phi-0.5)^2))

	ode_default_options()..., callback = callbacks, maxiters=1e7);
	ode_default_options()..., callback = callbacks, maxiters = 1e7);

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	function create_conduit_node(integrator, mesh::P4estMesh, equations, solver, cache, nvisnodes)
	function create_conduit_node(integrator, mesh::P4estMesh, equations, solver, cache,
	nvisnodes)

		varnames = Trixi.varnames(solution_variables_, equations)
		timestep = integrator.stats.naccept

	x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) : vec(interpolation_node_coordinates[1, :, :, :, :])
	x = (ndims_ == 2) ? vec(interpolation_node_coordinates[1, :, :, :]) :
	vec(interpolation_node_coordinates[1, :, :, :, :])

	y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) : vec(interpolation_node_coordinates[2, :, :, :, :])
	y = (ndims_ == 2) ? vec(interpolation_node_coordinates[2, :, :, :]) :
	vec(interpolation_node_coordinates[2, :, :, :, :])

	node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ? "quad" : "hex"
	node["catalyst/channels/input/data/topologies/mesh/elements/shape"] = (ndims_ == 2) ?
	"quad" : "hex"

	y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) : vec(node_coordinates[2, :, :, :, :])
	y = (ndims_ == 2) ? vec(node_coordinates[2, :, :, :]) :
	vec(node_coordinates[2, :, :, :, :])