Small improvements in make.jl and Na example.

cesmix-mit · Jul 5, 2024 · 1d8bf75 · 1d8bf75
1 parent 507cce3
commit 1d8bf75
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git 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
@@ -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")