Updates

docs/src/ecosystem/atomsbase.jl

@@ -52,13 +52,13 @@ scfres = self_consistent_field(basis, tol=1e-8);
 
 # ### Reading a system using AtomsIO
 #
+# Read a file using [AtomsIO](https://github.com/mfherbst/AtomsIO.jl),
+# which directly yields an AbstractSystem.
+#
 using AtomsIO
+system = load_system("Si.extxyz");
 
-## Read a file using [AtomsIO](https://github.com/mfherbst/AtomsIO.jl),
-## which directly yields an AbstractSystem.
-system = load_system("Si.extxyz")
-
-## Now run the LDA calculation:
+# Run the LDA calculation:
 pseudopotentials = Dict(:Si => "hgh/lda/si-q4")
 model  = model_DFT(system; pseudopotentials, functionals=LDA(), temperature=1e-3)
 basis  = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])

docs/src/ecosystem/input_output.jl

@@ -127,4 +127,4 @@ save_scfres("iron_afm.jld2", scfres)
 # (Cleanup files generated by this notebook.)
 rm.(["iron_afm.vts", "iron_afm.jld2",
      "iron_afm.json", "iron_afm_energies.json", "iron_afm_scfres.json",
-     "iron_afm_bands.json"])
+     "iron_afm_bands.json"]);

examples/pseudopotentials.jl

@@ -47,7 +47,7 @@ using Plots
 # package. See [the documentation of PseudoPotentialData](https://juliamolsim.github.io/PseudoPotentialData.jl/stable/)
 # for the list of available pseudopotential families.
 
-pseudopotentials_upf = PseudoFamily("dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf")
+pseudopotentials_upf = PseudoFamily("dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf");
 
 # Such a `PseudoFamily` object acts like a dictionary from an element symbol
 # to a pseudopotential file. They can be directly employed to select the
@@ -59,7 +59,7 @@ pseudopotentials_upf = PseudoFamily("dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf
 # a plain
 # `Dict` to map from atomic symbols to the employed pseudopotential file.
 # This we employ in combination with the HGH-type pseudopotentials:
-pseudopotentials_hgh = Dict(:Si => "hgh/lda/si-q4.hgh")
+pseudopotentials_hgh = Dict(:Si => "hgh/lda/si-q4.hgh");
 
 # First, we'll take a look at the energy cutoff convergence of these two pseudopotentials.
 # For both pseudos, a reference energy is calculated with a cutoff of 140 Hartree, and

src/elements.jl

@@ -84,15 +84,15 @@ local_potential_real(el::ElementCoulomb, r::Real) = -el.Z / r
 struct ElementPsp <: Element
     Z::Int         # Nuclear charge
     symbol::Symbol # Element symbol
-    mass           # Atomic mass
     psp            # Pseudopotential data structure
+    mass           # Atomic mass
 end
 function Base.show(io::IO, el::ElementPsp)
     pspid = isempty(el.psp.identifier) ? "custom" : el.psp.identifier
     if el.mass == atomic_mass(el)
-        print(io, "ElementPsp($(el.symbol); psp=\"$pspid\")")
+        print(io, "ElementPsp($(el.symbol), \"$pspid\")")
     else
-        print(io, "ElementPsp($(el.symbol); psp=\"$pspid\", mass=\"$(el.mass)\")")
+        print(io, "ElementPsp($(el.symbol), \"$pspid\"; mass=\"$(el.mass)\")")
     end
 end
 
@@ -130,7 +130,7 @@ function ElementPsp(symbol::Symbol, family::AbstractDict; mass=element(symbol).a
 end
 function ElementPsp(symbol::Symbol, psp; mass=element(symbol).atomic_mass)
     Z = periodic_table[symbol].number
-    ElementPsp(Z, symbol, mass, psp)
+    ElementPsp(Z, symbol, psp, mass)
 end
 ElementPsp(symbol::Symbol, psp::Nothing; kwargs...) = ElementCoulomb(symbol; kwargs...)
 ElementPsp(key, psp; kwargs...) = ElementPsp(Symbol(periodic_table[key].symbol), psp; kwargs...)

src/external/atoms_calculators.jl

@@ -33,7 +33,20 @@ end
 AtomsCalculators.energy_unit(::DFTKCalculator) = u"hartree"
 AtomsCalculators.length_unit(::DFTKCalculator) = u"bohr"
 
-# TODO DFTKCalculator needs a custom show function (both brief and detailed)
+function Base.show(io::IO, calc::DFTKCalculator)
+    fields = String[]
+    for key in (:functionals, :pseudopotentials, :temperature, :smearing)
+        if haskey(calc.params.model_kwargs, key)
+            push!(fields, "$key=$(getproperty(calc.params.model_kwargs, key))")
+        end
+    end
+    for key in (:Ecut, :kgrid)
+        if haskey(calc.params.basis_kwargs, key)
+            push!(fields, "$key=$(getproperty(calc.params.basis_kwargs, key))")
+        end
+    end
+    print(io, "DFTKCalculator($(join(fields, ", ")))")
+end
 
 """
 Construct a [AtomsCalculators](https://github.com/JuliaMolSim/AtomsCalculators.jl)