supercell business

louisponet · Jul 9, 2019 · 533da20 · 533da20
1 parent 2c6ce6d
commit 533da20
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Showing 4 changed files with 14 additions and 7 deletions.
diff --git a/src/API.jl b/src/API.jl
@@ -26,6 +26,8 @@ export searchinput, searchinputs, setcutoffs!, setname!
 export atom, atoms, setatoms!, setpseudos!, projections, setprojections!, cell,
 	   set_magnetization!
 
+export create_supercell
+
 # Atom interface functions
 for interface_function in (:name,
 						   :position_cart,

diff --git a/src/atom.jl b/src/atom.jl
@@ -121,7 +121,7 @@ Atom(name::Symbol, el::Symbol, args...; kwargs...) =
 	Atom(name, element(el), args...; kwargs...)
 
 #TODO this is a little iffy
-Atom(orig_at::Atom, new_pos_cart::Point3) = Atom(name(orig_at), element(orig_at), new_pos_cart, position_cryst(orig_at), pseudo(orig_at), projections(orig_at), magnetization(orig_at), dftu(orig_at))
+Atom(orig_at::Atom, new_pos_cart::Point3, new_pos_cryst::Point3) = Atom(name(orig_at), element(orig_at), new_pos_cart, new_pos_cryst, pseudo(orig_at), projections(orig_at), magnetization(orig_at), dftu(orig_at))
 #Easiest way to implement a new abstractatom is to provide a way to access
 #the struct holding `name`, `position_cart`, `element`, `pseudo`, `projection` fields
 atom(at::Atom) = at

diff --git a/src/jobAPI.jl b/src/jobAPI.jl
@@ -488,3 +488,6 @@ set_magnetization!(job::DFJob, args...) =
 
 Base.joinpath(job::DFJob, p) =
 	joinpath(job.local_dir, p)
+
+create_supercell(job::DFJob, args...) =
+	create_supercell(structure(job), args...)
diff --git a/src/structure.jl b/src/structure.jl
@@ -157,14 +157,16 @@ function create_supercell(structure::AbstractStructure, na::Int, nb::Int, nc::In
     orig_cell  = cell(structure)
     scale_mat  = diagm(0 => 1 .+ [na, nb, nc])
     new_cell   = orig_cell * scale_mat
-    new_atoms  = deepcopy(orig_ats)
+    new_atoms  = eltype(orig_ats)[]
     for ia=0:na, ib=0:nb, ic=0:nc
-        if all((ia, ib, ic) .== 0)
-            continue
-        end
-        transl_vec = orig_cell*[ia, ib, ic]
+        # if all((ia, ib, ic) .== 0)
+        #     continue
+        # end
+        transl_vec = orig_cell * [ia, ib, ic]
         for at in orig_ats
-            push!(new_atoms, Atom(at, position_cart(at)+transl_vec))
+	        cart_pos = position_cart(at) + transl_vec
+	        cryst_pos = inv(new_cell) * cart_pos
+            push!(new_atoms, Atom(at, cart_pos, Point3(cryst_pos)))
         end
     end
     return Structure(name(structure), Mat3(new_cell), new_atoms, data(structure))