diff --git a/docs/make.jl b/docs/make.jl index 3c29f630..2814cfd6 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -35,31 +35,36 @@ end # Basic examples examples = [ - "1 - Fit a-HfO2 dataset with ACE" => "ACE-aHfO2/fit-ace-ahfo2.jl", - "2 - Load Ar+Lennard-Jones dataset and postprocess" => "LJ-Ar/lennard-jones-ar.jl" + "Example 1 - Fit a-HfO2 dataset with ACE" => "ACE-aHfO2/fit-ace-ahfo2.jl", ] basic_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR) # Subsampling examples examples = [ - "1 - Subsample a-HfO2 dataset with DPP and fit with ACE" => "DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl", - "2 - Subsample Na dataset with DPP and fit with ACE" => "DPP-ACE-Na/fit-dpp-ace-na.jl", - "3 - Subsample Si dataset with DPP, fit with ACE, and cross validate" => "DPP-ACE-Si/fit-dpp-ace-si.jl", + "Example 1 - Subsample a-HfO2 dataset with DPP and fit with ACE" => "DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl", + "Example 2 - Subsample Na dataset with DPP and fit with ACE" => "DPP-ACE-Na/fit-dpp-ace-na.jl", + "Example 3 - Subsample Si dataset with DPP, fit with ACE, and cross validate" => "DPP-ACE-Si/fit-dpp-ace-si.jl", ] ss_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR) # Optimization examples examples = [ - "1 - Optimize ACE hyper-parameters: minimize force time and fitting error" => "Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl", + "Example 1 - Optimize ACE hyper-parameters: minimize force time and fitting error" => "Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl", ] opt_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR) # Dimension reduction examples examples = [ - "1 - Reduce ACE descriptors with PCA and fit a-HfO2 dataset" => "PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl", + "Example 1 - Reduce ACE descriptors with PCA and fit a-HfO2 dataset" => "PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl", ] dr_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR) +examples = [ + "Example 1 - Load Ar+Lennard-Jones dataset and postprocess" => "LJ-Ar/lennard-jones-ar.jl" +] +misc_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR) + + # Make and deploy docs ######################################################### makedocs( @@ -77,9 +82,10 @@ makedocs( pages = ["Home" => "index.md", "How to run the examples" => "how-to-run-the-examples.md", "Basic examples" => basic_examples, - "Optimize atomistic data via intelligent subsampling" => ss_examples, - "Optimize interatomic potential models via hyper-paramter optimization" => opt_examples, - "Optimize interatomic potential models via dimension reduction" => dr_examples, + "Intelligent subsampling" => ss_examples, + "Hyper-paramter optimization" => opt_examples, + "Dimension reduction" => dr_examples, + "Misc" => misc_examples, "API" => "api.md"], format = Documenter.HTML(; prettyurls = get(ENV, "CI", "false") == "true", diff --git a/examples/DPP-ACE-Na/fit-dpp-ace-na.jl b/examples/DPP-ACE-Na/fit-dpp-ace-na.jl index db7b70b6..fa7918a8 100644 --- a/examples/DPP-ACE-Na/fit-dpp-ace-na.jl +++ b/examples/DPP-ACE-Na/fit-dpp-ace-na.jl @@ -46,12 +46,12 @@ dpp = kDPP(ds_train, GlobalMean(), DotProduct(); batch_size = 200) # Subsample trainig dataset. dpp_inds = get_random_subset(dpp) -# ## Learn ACE coefficients based on ACE descriptors and DFT data. +# ## e. Learn ACE coefficients based on ACE descriptors and DFT data. lb = LBasisPotential(ace) α = 1e-8 Σ = learn!(lb, ds_train[dpp_inds], α) -# ## e. Post-process output: calculate metrics, create plots, and save results. +# ## f. Post-process output: calculate metrics, create plots, and save results. # Update test dataset by adding energy descriptors. println("Computing local descriptors of test dataset")