many updates

src/API.jl

@@ -25,13 +25,14 @@ export searchinput, searchinputs, setcutoffs!
 
 #Interacting with the Structure inside DFJob
 export atom, atoms, setatoms!, setpseudos!, projections, setprojections!, cell, a, b, c,
-	   set_magnetization!, symmetry_operators, international, niggli_reduce, update_geometry!
+	   set_magnetization!, symmetry_operators, international, niggli_reduce, update_geometry!,
+	   high_symmetry_kpath, high_symmetry_kpoints
 
 export create_supercell
 
 # Atom interface functions
 export name, position_cart, position_cryst, element, pseudo, projections, magnetization, dftu
-export distance, set_position!, scale_bondlength!
+export distance, set_position!, scale_bondlength!, polyhedron
 
 #Bands related functionality
 export bandgap

src/atom.jl

@@ -258,3 +258,16 @@ function scale_bondlength!(at1::AbstractAtom, at2::AbstractAtom, scale::Real, ce
 	set_position!(at1, new_p1, cell)
 	set_position!(at2, new_p2, cell)
 end
+
+"""
+    polyhedron(at::AbstractAtom, atoms::Vector{<:AbstractAtom}, order::Int)
+    polyhedron(at::AbstractAtom, str::AbstractStructure, order::Int)
+
+Returns a polyhedron around the atom, i.e. the `order` closest atoms.
+The returned atoms will be ordered according to their distance to the first one.
+In the case of a structure rather than a set of atoms, the search will
+be performed over all atoms in the structure.
+"""
+function polyhedron(at::AbstractAtom, atoms::Vector{<:AbstractAtom}, order::Int)
+    return sort(atoms, by = x -> distance(x, at))[1:order]
+end

src/display/glimpse.jl

@@ -3,6 +3,12 @@ const Gl = Glimpse
 
 function Gl.Diorama(str::AbstractStructure)
     dio = Diorama(name=Symbol(str.name))
+    add_structure!(dio, str)
+    dio[Gl.PointLight].data[1] = Gl.PointLight(diffuse=1.5f0, ambient=1.5f0)
+    Gl.center_cameras(dio)
+    return dio
+end
+function add_structure!(dio::Diorama, str::AbstractStructure)
     Entity(dio, Gl.assemble_wire_axis_box(position=zero(Point3f0), x=ustrip(a(str)), y=ustrip(b(str)), z=ustrip(c(str)), color=Gl.BLACK)...)
     for at in atoms(str)
         origin = Point3f0(ustrip(position_cart(at))...)
@@ -13,6 +19,5 @@ function Gl.Diorama(str::AbstractStructure)
             Entity(dio, Gl.assemble_arrow(origin, origin + Point3f0(magnetization(at)...), color=color, radius_ratio=1.5f0, thickness = 0.05f0)...)
         end
     end
-    dio[Gl.PointLight].data[1] = Gl.PointLight(diffuse=1.5f0, ambient=1.5f0)
-    expose(dio)
+    return dio
 end

src/fileio.jl

@@ -388,6 +388,7 @@ function read_job_inputs(job_file::String)
 	        elseif occursin("#SBATCH", line)
                 if occursin("-J", line)
                     name = split(line)[end]
+                    name = name == "-J" ? "noname" : name
                 else
                     push!(header, line)
                 end

src/jobAPI.jl

@@ -11,6 +11,10 @@ function save(job::DFJob, local_dir=job.local_dir; kwargs...)
         mkpath(local_dir)
         @info "$local_dir did not exist, it was created."
     end
+    if isempty(job.name)
+        @warn "Job had no name, changed it to: noname"
+        job.name = "noname"
+    end
     sanitize_magnetization!(job)
     sanitize_projections!(job)
     sanitizeflags!(job)
@@ -665,7 +669,8 @@ function pdos(job::DFJob, atsym::Symbol, filter_word="")
     end 
 end
 
-pdos(job::DFJob, atom::AbstractAtom, args...) = pdos(job, name(atom), args...)
+pdos(job::DFJob, atom::AbstractAtom, args...) =
+    pdos(job, name(atom), args...)
 
 function pdos(job::DFJob, atoms::Vector{AbstractAtom} = atoms(job), args...)
     t_energies, t_pdos = pdos(job, atoms[1], args...)
@@ -676,5 +681,9 @@ function pdos(job::DFJob, atoms::Vector{AbstractAtom} = atoms(job), args...)
     return (energies=t_energies, pdos=t_pdos)
 end
 
-update_geometry!(job::DFJob, new_str::AbstractStructure) = update_geometry!(job.structure, new_str)
+update_geometry!(job::DFJob, new_str::AbstractStructure) =
+    update_geometry!(job.structure, new_str)
+
+high_symmetry_kpath(j::DFJob, args...;kwargs...) =
+    high_symmetry_kpath(j.structure, args...; kwargs...)
 

src/plotting.jl

@@ -92,7 +92,7 @@ To plot multiple bands on one plot.
     end
 end
 
-@recipe function f(job::DFJob, ymin, ymax, occupy_ratio=0.2)
+@recipe function f(job::DFJob, ymin, ymax, occupy_ratio=0.2; overlap_spin=false)
     ylims --> [ymin, ymax]
     if !isQEjob(job)
         error("output plotting only implemented for QE jobs.")
@@ -109,7 +109,6 @@ end
     tick_vals = Int[]
     tick_syms = String[]
     kpoints = bands isa NamedTuple ? bands.up[1].k_points_cryst : bands[1].k_points_cryst
-    @show ks.kpoints
     for (i, k) in enumerate(kpoints)
         if ks!==nothing
             kpath = ks.kpoints
@@ -156,7 +155,7 @@ end
     # PDOS part
     projwfc = getfirst(x -> isprojwfccalc(x) && hasoutfile(x), inputs(job))
     if projwfc !== nothing
-        if bands isa NamedTuple
+        if bands isa NamedTuple && !overlap_spin
             doswindow = 3
             layout --> (1,3)
         else
@@ -242,13 +241,13 @@ end
                 lab = ""
             end
             for (ib, (b, c)) in enumerate(zip(bnds[window_ids], colors))
-                plot_band(b, c, ib == 1 ? lab : "", iplt)
+                plot_band(b, c, ib == 1 ? lab : "", overlap_spin ? 1 : iplt)
             end
         end
 
     # If no pdos is present
     else
-        if bands isa NamedTuple
+        if bands isa NamedTuple && !overlap_spin
             layout := (1,2)
         else
             layout := (1,1)
@@ -261,7 +260,7 @@ end
                 color = iplt == 1 ? :blue : :red
                 #loop over bands inside window
                 for (ib, b) in enumerate(bnds[window_ids])
-                    plot_band(b, color, ib == 1 ? lab : "", iplt)
+                    plot_band(b, color, ib == 1 ? lab : "", overlap_spin ? 1 : iplt)
                 end
             end
         else