Merge pull request ACEsuit#173 from ACEsuit/descriptor

Descriptor

Author: wcwitt

docs/src/tutorials/descriptor.jl

@@ -12,30 +12,27 @@ dataset, _, _ = ACEpotentials.example_dataset("Si_tiny");
 
 # An ACE basis specifies a vector of invariant features of atomic environments and can therefore be used as a general descriptor.
 
-basis = ACE1x.ace_basis( elements = [:Si],
-                          order = 3,        # body-order - 1
-                          totaldegree = 8, ); 
+basis = ACE1x.ace_basis(elements = [:Si],
+                        rcut = 5.5,
+                        order = 3,        # body-order - 1
+                        totaldegree = 8);
 
 # Compute an averaged structural descriptor for each configuration.
 
 descriptors = []
 config_types = []
 for atoms in dataset
-    descriptor = zeros(length(basis))
-    for i in 1:length(atoms)
-        descriptor += site_energy(basis, atoms, i)
-    end
-    descriptor /= length(atoms)
-    push!(descriptors, descriptor)
+    struct_descriptor = sum(site_descriptors(basis, atoms)) / length(atoms)
+    push!(descriptors, struct_descriptor)
     push!(config_types, atoms.data["config_type"].data)
 end
 
 # Finally, extract the descriptor principal components and plot. Note the segregation by configuration type.
 
-descriptors1 = hcat(descriptors...)
-M = fit(PCA, descriptors1; maxoutdim=3, pratio=1)
-descriptors_trans = transform(M, descriptors1)
+descriptors = hcat(descriptors...)
+M = fit(PCA, descriptors; maxoutdim=3, pratio=1)
+descriptors_trans = transform(M, descriptors)
 p = scatter(
     descriptors_trans[1,:], descriptors_trans[2,:], descriptors_trans[3,:],
     marker=:circle, linewidth=0, group=config_types, legend=:right)
-plot!(p, xlabel="PC1", ylabel="PC2", zlabel="PC3", camera=(40,10))
+plot!(p, xlabel="PC1", ylabel="PC2", zlabel="PC3", camera=(20,10))

src/ACEpotentials.jl

@@ -11,6 +11,7 @@ include("atoms_data.jl")
 include("model.jl")
 include("export.jl")
 include("example_data.jl")
+include("descriptor.jl")
 
 include("analysis/potential_analysis.jl")
 include("analysis/dataset_analysis.jl")

src/descriptor.jl

@@ -0,0 +1,22 @@
+export site_descriptor, site_descriptors
+
+
+"""
+    site_descriptor(basis, atoms::AbstractAtoms, i::Integer)
+
+Compute the site descriptor for the `i`th atom in `atoms`.
+"""
+function site_descriptor(basis, atoms::AbstractAtoms, i::Integer)
+   return site_energy(basis, atoms, i)
+end
+
+
+"""
+    site_descriptors(basis, atoms::AbstractAtoms)
+
+Compute site descriptors for all atoms in `atoms`, returning them as
+a vector of vectors.
+"""
+function site_descriptors(basis, atoms::AbstractAtoms)
+    return [site_descriptor(basis, atoms, i) for i in 1:length(atoms)]
+end