Removed type restriction to AbstractSystem in functions.

src/atomsbase_interface.jl

@@ -17,6 +17,21 @@ function update_positions(system, positions::AbstractVector{<:AbstractVector{<:U
     AbstractSystem(system; particles)
 end
 
+@doc raw"""
+Creates a new system based on ``system`` but with atoms positions and lattice vectors 
+updated to the ones provided. 
+New atomic positions and lattice vectors should be provided in a ComponentArray 
+with components `positions` and `lattice` respectively, the lattice 
+vectors being given as a vector of vectors.
+
+"""
+function update_positions(system, 
+                          generalized_positions::ComponentVector{<:Unitful.Length})
+    particles = [Atom(atom; position) for (atom, position)
+                 in zip(system, generalized_positions.positions)]
+    AbstractSystem(system; particles, generalized_positions.bounding_box)
+end
+
 @doc raw"""
 Creates a new system based on ``system`` where the non clamped positions are
 updated to the ones provided (in the order in which they appear in the system).

src/optimization.jl

@@ -12,7 +12,7 @@ export minimize_energy
     are used.
 
 """
-function Optimization.OptimizationFunction(system::AbstractSystem, calculator; kwargs...)
+function Optimization.OptimizationFunction(system, calculator; kwargs...)
     mask = not_clamped_mask(system)  # mask is assumed not to change during optim.
 
     f = function(x::AbstractVector{<:Real}, p)
@@ -35,10 +35,35 @@ function Optimization.OptimizationFunction(system::AbstractSystem, calculator; k
     OptimizationFunction(f; grad=g!)
 end
 
-function minimize_energy(system::AbstractSystem, calculator; solver=Optim.LBFGS(), kwargs...)
+function minimize_energy(system, calculator; solver=Optim.LBFGS(), kwargs...)
     # Use current system parameters as starting positions.
     x0 = austrip.(not_clamped_positions(system)) # Optim modifies x0 in-place, so need a mutable type.
     f_opt = OptimizationFunction(system, calculator)
     problem = OptimizationProblem(f_opt, x0, nothing)  # Last argument needed in Optimization.jl.
     solve(problem, solver; kwargs...)
 end
+
+# TODO: temporary name. This performs structural relaxation allowing atoms as well as unit cell 
+# vectors to move.
+function OptimizationFunctionVariableCell(system, calculator; kwargs...)
+    mask = not_clamped_mask(system)  # mask is assumed not to change during optim.
+
+    f = function(x::AbstractVector{<:Real}, p)
+        new_system = update_not_clamped_positions(system, x * u"bohr")
+        energy = AtomsCalculators.potential_energy(new_system, calculator; kwargs...)
+        austrip(energy)
+    end
+
+    g! = function(G::AbstractVector{<:Real}, x::AbstractVector{<:Real}, p)
+        new_system = update_not_clamped_positions(system, x * u"bohr")
+        energy = AtomsCalculators.potential_energy(new_system, calculator; kwargs...)
+
+        forces = AtomsCalculators.forces(new_system, calculator; kwargs...)
+        # Translate the forces vectors on each particle to a single gradient for the optimization parameter.
+        forces_concat = collect(Iterators.flatten(forces[mask]))
+
+        # NOTE: minus sign since forces are opposite to gradient.
+        G .= - austrip.(forces_concat)
+    end
+    OptimizationFunction(f; grad=g!)
+end