Add ZBL to Vref #737
Annotations
10 errors and 2 warnings
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:40-49
```@example basic_julia_workflow
hyperparams = (elements = [:Ti, :Al],
order = 3,
totaldegree = 6,
rcut = 5.5,
Eref = [:Ti => -1586.0195, :Al => -105.5954])
model = ace1_model(; hyperparams...)
@show length_basis(model);
nothing #hide
```
exception =
UndefVarError: `E0s` not defined
Stacktrace:
[1] ace_model(rbasis::ACEpotentials.Models.SplineRnlrzzBasis{2, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 30, Float64}, Ytype::Symbol, AA_spec::Vector{Vector{@NamedTuple{n::Int64, l::Int64, m::Int64}}}, level::ACEpotentials.Models.TotalDegree, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{2, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 12, Float64}, Vref::ACEpotentials.Models.OneBody{Float64, Unitful.FreeUnits{(), NoDims, nothing}, Unitful.FreeUnits{(Å,), 𝐋, nothing}})
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace.jl:155
[2] ace_model(; elements::Vector{Symbol}, order::Int64, Ytype::Symbol, ZBL::Bool, E0s::Dict{Symbol, Unitful.Quantity{Float64, 𝐋^2 𝐌 𝐓^-2, Unitful.FreeUnits{(eV,), 𝐋^2 𝐌 𝐓^-2, nothing}}}, rin0cuts::StaticArraysCore.SMatrix{2, 2, @NamedTuple{rin::Float64, r0::Float64, rcut::Float64}, 4}, rbasis::ACEpotentials.Models.SplineRnlrzzBasis{2, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 30, Float64}, rbasis_type::Symbol, maxl::Int64, maxn::Int64, maxq_fact::Float64, maxq::Symbol, init_Wradial::Symbol, level::ACEpotentials.Models.TotalDegree, max_level::Vector{Int64}, init_WB::Symbol, pair_maxn::Nothing, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{2, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 12, Float64}, pair_learnable::Bool, pair_transform::Tuple{Symbol, Int64, Int64}, init_Wpair::Symbol, rng::Random.TaskLocalRNG)
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace_heuristics.jl:216
[3] ace1_model(; kwargs::@kwargs{elements::Vector{Symbol}, order::Int64, totaldegree::Int64, rcut::Float64, Eref::Vector{Pair{Symbol, Float64}}})
@ ACEpotentials.ACE1compat ~/work/ACEpotentials.jl/ACEpotentials.jl/src/ace1_compat.jl:384
[4] top-level scope
@ basic_julia_workflow.md:46
[5] eval
@ ./boot.jl:385 [inlined]
[6] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[7] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[8] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[10] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[11] with_logger
@ ./logging.jl:627 [inlined]
[12] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:78-80
```@example basic_julia_workflow
P = algebraic_smoothness_prior(model; p = 4) # (p = 4 is in fact the default)
```
exception =
UndefVarError: `model` not defined
Stacktrace:
[1] top-level scope
@ basic_julia_workflow.md:79
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
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../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:84-87
```@example basic_julia_workflow
result = acefit!(train_data, model; solver=solver, prior = P, weights=weights);
nothing #hide
```
exception =
UndefVarError: `P` not defined
Stacktrace:
[1] top-level scope
@ basic_julia_workflow.md:85
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:91-95
```@example basic_julia_workflow
@info("Training Error Table")
err_train = ACEpotentials.linear_errors(train_data, model; weights=weights);
nothing #hide
```
exception =
UndefVarError: `model` not defined
Stacktrace:
[1] top-level scope
@ basic_julia_workflow.md:92
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:99-103
```@example basic_julia_workflow
@info("Test Error Table")
err_test = ACEpotentials.linear_errors(test_data, model; weights=weights);
nothing #hide
```
exception =
UndefVarError: `model` not defined
Stacktrace:
[1] top-level scope
@ basic_julia_workflow.md:100
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/basic_julia_workflow.md:107-112
```@example basic_julia_workflow
using JSON
open("TiAl_model.json", "w") do f
JSON.print(f, Dict("hyperparams" => hyperparams, "params" => model.ps))
end
```
exception =
UndefVarError: `model` not defined
Stacktrace:
[1] (::Main.__atexample__named__basic_julia_workflow.var"#1#2")(f::IOStream)
@ Main.__atexample__named__basic_julia_workflow ./basic_julia_workflow.md:110
[2] open(::Main.__atexample__named__basic_julia_workflow.var"#1#2", ::String, ::Vararg{String}; kwargs::@kwargs{})
@ Base ./io.jl:396
[3] open(::Function, ::String, ::String)
@ Base ./io.jl:393
[4] top-level scope
@ basic_julia_workflow.md:109
[5] eval
@ ./boot.jl:385 [inlined]
[6] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[7] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[8] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[10] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[11] with_logger
@ ./logging.jl:627 [inlined]
[12] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/dataset_analysis.md:54-64
```@example dataset_analysis
r_cut_ul = ustrip(u"Å", r_cut)
model1 = ace1_model(elements = [:Si,], order = 3,
totaldegree = 10, rcut = r_cut_ul)
model2 = ace1_model(elements = [:Si,], order = 3,
totaldegree = 10, rcut = r_cut_ul,
transform = (:agnesi, 2, 2) );
nothing #hide
```
exception =
UndefVarError: `E0s` not defined
Stacktrace:
[1] ace_model(rbasis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 37, Float64}, Ytype::Symbol, AA_spec::Vector{Vector{@NamedTuple{n::Int64, l::Int64, m::Int64}}}, level::ACEpotentials.Models.TotalDegree, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 10, Float64}, Vref::ACEpotentials.Models.OneBody{Float64, Unitful.FreeUnits{(), NoDims, nothing}, Unitful.FreeUnits{(Å,), 𝐋, nothing}})
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace.jl:155
[2] ace_model(; elements::Vector{Symbol}, order::Int64, Ytype::Symbol, ZBL::Bool, E0s::Nothing, rin0cuts::StaticArraysCore.SMatrix{1, 1, @NamedTuple{rin::Float64, r0::Float64, rcut::Float64}, 1}, rbasis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 37, Float64}, rbasis_type::Symbol, maxl::Int64, maxn::Int64, maxq_fact::Float64, maxq::Symbol, init_Wradial::Symbol, level::ACEpotentials.Models.TotalDegree, max_level::Vector{Int64}, init_WB::Symbol, pair_maxn::Nothing, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 10, Float64}, pair_learnable::Bool, pair_transform::Tuple{Symbol, Int64, Int64}, init_Wpair::Symbol, rng::Random.TaskLocalRNG)
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace_heuristics.jl:216
[3] ace1_model(; kwargs::@kwargs{elements::Vector{Symbol}, order::Int64, totaldegree::Int64, rcut::Float64})
@ ACEpotentials.ACE1compat ~/work/ACEpotentials.jl/ACEpotentials.jl/src/ace1_compat.jl:384
[4] top-level scope
@ dataset_analysis.md:57
[5] eval
@ ./boot.jl:385 [inlined]
[6] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[7] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[8] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[10] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[11] with_logger
@ ./logging.jl:627 [inlined]
[12] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/dataset_analysis.md:69-89
```@example dataset_analysis
using ForwardDiff
trans1, trans1_pair = ACEpotentials.get_transforms(model1)
trans2, trans2_pair = ACEpotentials.get_transforms(model2)
∇t1 = r -> ForwardDiff.derivative(trans1[(:Si, :Si)], r)
∇t2 = r -> ForwardDiff.derivative(trans2[(:Si, :Si)], r)
rp = range(0.0, r_cut_ul, length = 200)
plt_t = plot(rp, abs.(∇t1.(rp)), lw=3,
xlabel = L"r [\AA]", label = L"|t_1'(r)|",
yticks = [], ylabel = "", xlims = (0, r_cut_ul))
plot!(plt_t, rp, abs.(∇t2.(rp)), lw=3, label = L"|t_2'(r)")
vline!([ustrip(rnn(:Si)),], lw=2, label = L"r_{\rm nn}")
plt_rdf = histogram(rdf[(:Si, :Si)], bins=100, label = "rdf",
xlabel = L"r [\AA]", ylabel = "RDF",
yticks = [], xlims = (0, r_cut_ul))
vline!([ustrip(rnn(:Si)),], label = L"r_{\rm nn}", lw=3)
plot(plt_t, plt_rdf, layout=grid(2, 1, heights=[0.7, 0.3]), size = (800, 400))
```
exception =
UndefVarError: `model1` not defined
Stacktrace:
[1] top-level scope
@ dataset_analysis.md:71
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
|
|
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/descriptor.md:24-30
```@example descriptor
model = ace1_model(elements = [:Si],
rcut = 5.5,
order = 3, # body-order - 1
totaldegree = 8);
nothing #hide
```
exception =
UndefVarError: `E0s` not defined
Stacktrace:
[1] ace_model(rbasis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 24, Float64}, Ytype::Symbol, AA_spec::Vector{Vector{@NamedTuple{n::Int64, l::Int64, m::Int64}}}, level::ACEpotentials.Models.TotalDegree, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 8, Float64}, Vref::ACEpotentials.Models.OneBody{Float64, Unitful.FreeUnits{(), NoDims, nothing}, Unitful.FreeUnits{(Å,), 𝐋, nothing}})
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace.jl:155
[2] ace_model(; elements::Vector{Symbol}, order::Int64, Ytype::Symbol, ZBL::Bool, E0s::Nothing, rin0cuts::StaticArraysCore.SMatrix{1, 1, @NamedTuple{rin::Float64, r0::Float64, rcut::Float64}, 1}, rbasis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.PolyEnvelope2sX{Float64}, 24, Float64}, rbasis_type::Symbol, maxl::Int64, maxn::Int64, maxq_fact::Float64, maxq::Symbol, init_Wradial::Symbol, level::ACEpotentials.Models.TotalDegree, max_level::Vector{Int64}, init_WB::Symbol, pair_maxn::Nothing, pair_basis::ACEpotentials.Models.SplineRnlrzzBasis{1, ACEpotentials.Models.NormalizedTransform{Float64, ACEpotentials.Models.GeneralizedAgnesiTransform{Float64}}, ACEpotentials.Models.ACE1_PolyEnvelope1sR{Float64}, 8, Float64}, pair_learnable::Bool, pair_transform::Tuple{Symbol, Int64, Int64}, init_Wpair::Symbol, rng::Random.TaskLocalRNG)
@ ACEpotentials.Models ~/work/ACEpotentials.jl/ACEpotentials.jl/src/models/ace_heuristics.jl:216
[3] ace1_model(; kwargs::@kwargs{elements::Vector{Symbol}, rcut::Float64, order::Int64, totaldegree::Int64})
@ ACEpotentials.ACE1compat ~/work/ACEpotentials.jl/ACEpotentials.jl/src/ace1_compat.jl:384
[4] top-level scope
@ descriptor.md:25
[5] eval
@ ./boot.jl:385 [inlined]
[6] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[7] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[8] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[10] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[11] with_logger
@ ./logging.jl:627 [inlined]
[12] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/literate_tutorials/descriptor.md:34-42
```@example descriptor
descriptors = []
config_types = []
for sys in dataset
sys_descriptor = sum(site_descriptors(sys, model)) / length(sys)
push!(descriptors, sys_descriptor)
push!(config_types, sys[:config_type])
end
```
exception =
UndefVarError: `model` not defined
Stacktrace:
[1] top-level scope
@ ./descriptor.md:38
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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