Update docs

docs/src/apireference.md

@@ -4,6 +4,9 @@ CurrentModule = GeometryOptimization
 
 # API reference
 
+```@index
+```
+
 ```@autodocs
 Modules = [GeometryOptimization]
 ```

docs/src/examples/aluminium_dftk.md

@@ -20,16 +20,18 @@ using DFTK
 
 model_kwargs = (; functionals=[:lda_x, :lda_c_pw], temperature=1e-3)
 basis_kwargs = (; kgrid=(3, 3, 3), Ecut=10.0)
-scf_kwargs   = (; tol=1e-5, mixing=KerkerMixing())
-calc = DFTKCalculator(; model_kwargs, basis_kwargs, scf_kwargs, verbose=true);
+scf_kwargs   = (; tol=1e-6, mixing=KerkerMixing())
+calc = DFTKCalculator(; model_kwargs, basis_kwargs, scf_kwargs, verbose=true)
+nothing
 ```
 
 We attach pseudopotentials to the aluminium system,
 i.e. we tell DFTK, that each aluminium atom should be modelled using
 a pseudopotential rather than the full Coulomb potential.
 
 ```@example dftk-aluminium
-system = attach_psp(system; Al="hgh/lda/al-q3");
+system = attach_psp(system; Al="hgh/lda/al-q3")
+nothing
 ```
 
 !!! info "Crude computational parameters"
@@ -49,6 +51,11 @@ GO = GeometryOptimization
 results = minimize_energy!(system, calc, GO.OptimLBFGS();
                            tol_force=1e-4u"eV/Å",
                            show_trace=true)
+nothing
+```
+
+The final energy is
+```@example dftk-aluminium
 results.energy
 ```
 

docs/src/examples/tial_lj.md

@@ -10,29 +10,29 @@ using EmpiricalPotentials
 using GeometryOptimization
 GO = GeometryOptimization
 
-system = load_system(joinpath(pkgdir(EmpiricalPotentials), "data/TiAl-1024.xyz")
-
-# Convert to AbstractSystem, so we have the `particles` attribute.
-particles = map(system) do atom
-    Atom(; pairs(atom)...)
-end
-system = AbstractSystem(data; particles)
+system = load_system(joinpath(pkgdir(EmpiricalPotentials), "data/TiAl-1024.xyz"))
+nothing
 ```
 
 Setup calculator:
 ```@example tial
 using Unitful
 using UnitfulAtomic
 calc = LennardJones(-1.0u"meV", 3.1u"Å", 13, 13, 6.0u"Å")
+nothing
 ```
 
 Minimise energy:
-```@example tial
+```julia
+## TODO: Should run as @example once EmpiricalPotentials is compatible
+
 results = minimize_energy!(system, calc, GO.OptimCG(); maxiters=10, show_trace=true)
 results.energy
 ```
 
 Final structure:
-```@example tial
+```julia
+## TODO: Should run as @example once EmpiricalPotentials is compatible
+
 results.system
 ```

docs/src/index.md

@@ -45,7 +45,3 @@ calculators to employ.
 Note that [`minimize_energy!`](@ref) supports further arguments to fine-tune the
 convergence tolerance or customise the solver selection.
 See the API documentation or the examples to explore this.
-
-
-```@index
-```

src/GeometryOptimization.jl

@@ -22,7 +22,7 @@ $(TYPEDSIGNATURES)
 $(DOCSTRING)
 """
 
-include("atomsbase_interface.jl")
+include("clamping_updating_positions.jl")
 include("optimization.jl")
 
 end

src/atomsbase_interface.jl → src/clamping_updating_positions.jl

@@ -4,11 +4,22 @@
 #
 export clamp_atoms
 
+"""
+Convert the input system to a kind of system we can work with, i.e. one where
+we have the `particles` keyword argument for setting new particles and positions.
+"""
+function convert_to_updatable(system)
+    if length(system) > 0 && !(system[1] isa Atom)
+        particles = [Atom(; pairs(atom)...) for atom in system]
+        AbstractSystem(system; particles)
+    else
+        system
+    end
+end
 
 """
 Creates a new system based on ``system`` but with atoms positions updated 
 to the ones provided.
-
 """
 function update_positions(system, positions::AbstractVector{<:AbstractVector{<:Unitful.Length}})
     particles = [Atom(atom; position) for (atom, position) in zip(system, positions)]
@@ -52,6 +63,6 @@ indices corresponding to their positions in the system.
 function clamp_atoms(system, clamped_indexes::Union{AbstractVector{<:Integer},Nothing})
     clamped = falses(length(system))
     clamped[clamped_indexes] .= true
-    particles = [Atom(atom; clamped=m) for (atom, m) in zip(system, clamped)]
-    AbstractSystem(system, particles=particles)
+    particles = [Atom(atom; clamped=msk) for (atom, msk) in zip(system, clamped)]
+    AbstractSystem(system; particles)
 end

src/optimization.jl

@@ -94,6 +94,8 @@ function minimize_energy!(system, calculator, solver;
                           tol_virial=1e-6u"eV",   # TODO How reasonable ?
                           callback=(x,y) -> false,
                           kwargs...)
+    system = convert_to_updatable(system)
+
     geoopt_state = GeometryOptimizationState(system, calculator)
     problem = OptimizationProblem(system, calculator, geoopt_state; sense=Optimization.MinSense)
     converged = false