fixed so now you should be able to have multiple atoms of the same kind

src/file_processing.jl

@@ -172,7 +172,7 @@ function read_qe_input(filename,T=Float32)
   control_blocks = Dict{Symbol,Dict{Symbol,Any}}()
   cell_param     = Dict{Symbol,Any}()
   pseudos        = Dict{Symbol,String}()
-  atoms          = Dict{Symbol,Point3D}()
+  atoms          = Dict{Symbol,Array{<:Point3D,1}}()
   k_dict         = Dict{Symbol,Any}()
 
   open(filename) do f
@@ -236,7 +236,11 @@ function read_qe_input(filename,T=Float32)
           line_segs = split(line)
           atom = Symbol(line_segs[1])
           position=Point3D(parse(T,line_segs[2]),parse(T,line_segs[3]),parse(T,line_segs[4]))
-          atoms[atom] = position
+          if !haskey(atoms,atom)
+            atoms[atom]=[position]
+          else
+            push!(atoms[atom],position)
+          end
           line = readline(f)
         end
         @goto startlabel        
@@ -264,6 +268,8 @@ function read_qe_input(filename,T=Float32)
   return DFInput(:QE,control_blocks,pseudos,cell_param,atoms,k_dict)
 end
 
+
+# change atom writing!
 """
 Writes a Quantum Espresso input file.
 
@@ -309,8 +315,10 @@ function write_qe_input(filename::String,df_input::DFInput)
 
       if !isempty(df_input.atoms)
         write(f,"ATOMIC_POSITIONS (crystal)\n")
-        for (atom,point) in df_input.atoms
-          write(f,"$(String(atom))    $(point.x)    $(point.y)    $(point.z) \n")
+        for (atom,points) in df_input.atoms
+          for point in points
+            write(f,"$(String(atom))    $(point.x)    $(point.y)    $(point.z) \n")
+          end
         end
         write(f,"\n")
       end

src/types.jl

@@ -32,7 +32,7 @@ mutable struct DFInput
   control_blocks::Dict{Symbol,Dict{Symbol,Any}}
   pseudos::Dict{Symbol,String}
   cell_param::Dict{Symbol,Any}
-  atoms::Dict{Symbol,Any}
+  atoms::Dict{Symbol,Array{<:Point3D,1}}
   k_points::Dict{Symbol,Any}
 end
 

test/file_processing_tests.jl

@@ -9,7 +9,7 @@ projwfc_input = read_qe_input(joinpath(@__DIR__,"../assets/inputs/qe/projwfc.in"
 @test scf_input.pseudos[:Te] == "Te.rel-pbesol-dn-kjpaw_psl.0.2.2.UPF"
 @test scf_input.k_points[:option] == :automatic
 @test scf_input.k_points[:nk3] == 10
-@test scf_input.atoms[:Te] == Point3D{Float64}(0.523252856, 0.523252856, 0.523252856)
+@test scf_input.atoms[:Te] == [Point3D{Float64}(0.523252856, 0.523252856, 0.523252856)]
 
 @test bands_input.control_blocks[:control][:calculation] == "'bands'"
 @test bands_input.pseudos[:Te] == scf_input.pseudos[:Te]

test/job_control_tests.jl

@@ -2,6 +2,7 @@ using DFControl, Base.Test
 TT = STDOUT
 redirect_stdout()
 
+
 df_job = load_qe_job("test_job",joinpath(@__DIR__,"../assets/inputs/qe"))
 df_job2 = load_qe_job("test_job",joinpath(@__DIR__,"../assets/inputs/qe"),new_homedir="blabla")
 @test df_job2.home_dir    == "blabla/"
@@ -10,7 +11,6 @@ df_job2 = load_qe_job("test_job",joinpath(@__DIR__,"../assets/inputs/qe"),new_ho
 @test df_job.home_dir     == joinpath(@__DIR__,"../assets/inputs/qe/")
 
 mkdir(joinpath(@__DIR__,"../assets/inputs/qe/test_dir/"))
-
 test_dir = joinpath(@__DIR__,"../assets/inputs/qe/test_dir/") 
 df_job.home_dir = test_dir 
 save_job(df_job)
@@ -44,13 +44,13 @@ change_job_data!(df_job,change_data2)
 check_keys = Symbol[:sk1,:prefix,:noncolin,:ecutwfc] 
 @test check_job_data(df_job,check_keys) == Dict(:sk1=>3,:prefix=>"'test'",:noncolin => false, :ecutwfc=> 35)
 
-set_data1 = Dict(:Ze => Point3D(1.2,3.2,1.2))
+set_data1 = Dict(:Ze => [Point3D(1.2,3.2,1.2)])
 set_data2 = Dict(:control => Dict(:test => true))
 set_job_data!(df_job,["bands","scf"],:atoms,set_data1)
 set_job_data!(df_job,["bands","scf"],:control_blocks,set_data2)
 @test df_job.calculations["bands"].control_blocks[:control][:test]
 @test df_job.calculations["scf"].control_blocks[:control][:pseudo_dir] == "'./'"
-@test df_job.calculations["scf"].atoms[:Ze] == Point3D(1.2,3.2,1.2)
+@test df_job.calculations["scf"].atoms[:Ze] == [Point3D(1.2,3.2,1.2)]
 
 redirect_stdout(TT)
 println("")

test/runtests.jl

@@ -6,8 +6,6 @@ using Base.Test
 
 tic()
 @testset "File processing tests" begin include("file_processing_tests.jl") end
-@testset "Job control tests" begin
-  include("job_control_tests.jl")
-end
+@testset "Job control tests" begin include("job_control_tests.jl") end
 @testset "Plotting tests" begin include("plotting_tests.jl") end
 toc()