Collection of some documentation extensions and bugfixes (JuliaMolSim…

…#873)

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.9
+current_version = 0.6.10
 commit = True
 tag = False
 

Project.toml

@@ -1,7 +1,7 @@
 name = "DFTK"
 uuid = "acf6eb54-70d9-11e9-0013-234b7a5f5337"
 authors = ["Michael F. Herbst <[email protected]>", "Antoine Levitt <[email protected]>"]
-version = "0.6.9"
+version = "0.6.10"
 
 [deps]
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"

examples/custom_potential.jl

@@ -29,6 +29,10 @@ function DFTK.local_potential_fourier(el::CustomPotential, q::Real)
     -el.α * exp(- (q * el.L)^2 / 2)
 end
 
+# !!! tip "Gaussian potentials and DFTK"
+#     DFTK already implements `CustomPotential` in form of the [`DFTK.ElementGaussian`](@ref),
+#     so this explicit re-implementation is only provided for demonstration purposes.
+
 # We set up the lattice. For a 1D case we supply two zero lattice vectors
 a = 10
 lattice = a .* [[1 0 0.]; [0 0 0]; [0 0 0]];

examples/pseudopotentials.jl

@@ -40,11 +40,15 @@ using LazyArtifacts
 import Main: @artifact_str # hide
 
 # Here, we will use a Perdew-Wang LDA PSP from [PseudoDojo](http://www.pseudo-dojo.org/),
-# which is available in the JuliaMolSim
-# [PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary).
+# which is available in the
+# [JuliaMolSim PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary).
 # Directories in PseudoLibrary correspond to artifacts that you can load using `artifact`
 # strings which evaluate to a filepath on your local machine where the artifact has been
 # downloaded.
+#
+# !!! note "Using the PseudoLibrary in your own calculations"
+#     Instructions for using the [PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary)
+#     in your own calculations can be found in its documentation.
 
 # We load the HGH and UPF PSPs using `load_psp`, which determines the
 # file format using the file extension. The `artifact` string literal resolves to the

src/eigen/diag.jl

@@ -53,8 +53,8 @@ function diagonalize_all_kblocks(eigensolver, ham::Hamiltonian, nev_per_kpoint::
         @assert size(ψguessk) == (n_Gk, nev_per_kpoint)
 
         prec = nothing
-        !isnothing(prec_type) && (prec = prec_type(ham.basis, kpt))
-        results[ik] = eigensolver(ham.blocks[ik], ψguessk;
+        !isnothing(prec_type) && (prec = prec_type(ham[ik]))
+        results[ik] = eigensolver(ham[ik], ψguessk;
                                   prec, tol, miniter, maxiter, n_conv_check)
 
         # Update progress bar if desired

src/eigen/preconditioners.jl

@@ -17,7 +17,8 @@ precondprep!(P, X) = P  # This API is also used in Optim.jl
 No preconditioning
 """
 struct PreconditionerNone end
-PreconditionerNone(basis, kpt) = I
+PreconditionerNone(::PlaneWaveBasis, ::Kpoint) = I
+PreconditionerNone(::HamiltonianBlock) = I
 
 """
 (simplified version of) Tetter-Payne-Allan preconditioning
@@ -41,6 +42,9 @@ function PreconditionerTPA(basis::PlaneWaveBasis{T}, kpt::Kpoint; default_shift=
     kin = kinetic_energy(kinetic_term, basis.Ecut, Gplusk_vectors_cart(basis, kpt))
     PreconditionerTPA{T}(basis, kpt, kin, nothing, default_shift)
 end
+function PreconditionerTPA(ham::HamiltonianBlock; kwargs...)
+    PreconditionerTPA(ham.basis, ham.kpoint)
+end
 
 @views function ldiv!(Y, P::PreconditionerTPA, R)
     if P.mean_kin === nothing

src/scf/nbands_algorithm.jl

@@ -81,6 +81,7 @@ function determine_n_bands(bands::AdaptiveBands, occupation::AbstractVector,
 
     # Determine number of bands to be computed
     n_bands_compute_ε = maximum(eigenvalues) do εk
+        n_bands_converge > length(εk) && return length(εk) + 1
         something(findlast(εnk -> εnk ≥ εk[n_bands_converge] + bands.gap_min, εk),
                   length(εk) + 1)
     end