fixes

src/DFControl.jl

@@ -85,6 +85,6 @@ module DFControl
 #     else
 #       error("DFControl not properly installed. Please run Pkg.build(\"DFControl\")")
 # end
-    include("precompile.jl")
-    _precompile_()
+    # include("precompile.jl")
+    # _precompile_()
 end

src/inputAPI.jl

@@ -128,12 +128,13 @@ runcommand(input::DFInput) = input.execs[1]
 
 "Returns the outputdata for the input."
 function outputdata(input::DFInput; print=true, overwrite=true)
-    if hasoutput(input) && !overwrite
-        return outdata(input)
-    end
-    if hasoutfile(input)
-        input.outdata = readoutput(input)
-        return input.outdata
+    if hasoutput(input)
+        if !overwrite && !isempty(outdata(input))
+            return outdata(input)
+        else
+            input.outdata = readoutput(input)
+            return input.outdata
+        end
     end
     print && (@warn "No output data or output file found for input: $(name(input)).")
     return SymAnyDict()

src/job.jl

@@ -292,5 +292,5 @@ function Base.pop!(job::DFJob, name::String)
     return out
 end
 
-find_files(job::DFJob, str::AbstractString) = joinpath.((job,), searchdir(job.local_dir, str))
+searchdir(job::DFJob, str::AbstractString) = joinpath.((job,), searchdir(job.local_dir, str))
 

src/jobAPI.jl

@@ -303,7 +303,7 @@ function outputdata(job::DFJob, inputs::Vector{DFInput}; print=true, onlynew=fal
             datadict[name(input)] = tout
         end
     end
-    datadict
+    return datadict
 end
 outputdata(job::DFJob; kwargs...) = outputdata(job, inputs(job); kwargs...)
 outputdata(job::DFJob, names::String...; kwargs...) =
@@ -528,20 +528,20 @@ Calculates the bandgap (possibly indirect) around the fermi level.
 Uses the first found bands calculation, if there is none it uses the first found nscf calculation.
 """
 function bandgap(job::DFJob, fermi=nothing)
-	band_calcs = getfirst.((isbandscalc, isnscfcalc, isscfcalc), (inputs(job),))
+	band_calcs = getfirst.([isbandscalc, isnscfcalc, isscfcalc], (inputs(job),))
 	if all(x -> x === nothing, band_calcs)
 		error("No valid calculation found to calculate the bandgap.\nMake sure the job has either a valid bands or nscf calculation.")
 	end
-	bands = readbands(getfirst(x -> x!==nothing, band_calcs))
 	if fermi === nothing
-    	fermi_calcs = getfirst.((isnscfcalc, isscfcalc), (inputs(job),))
+    	fermi_calcs = getfirst.([isnscfcalc, isscfcalc], (inputs(job),))
     	if all(x -> x === nothing, band_calcs)
     		error("No valid calculation found to extract the fermi level.\nPlease supply the fermi level manually.")
 		end
-		fermi = readfermi(getfirst(x -> x!==nothing, fermi_calcs))
+		fermi = maximum(readfermi.(filter(x -> x!==nothing, fermi_calcs)))
 	end
 
-	return bandgap(bands, fermi)
+	bands = readbands.(filter(x -> x!==nothing, band_calcs))
+	return minimum(bandgap.(bands, fermi))
 end
 
 "Searches for the first scf or nscf calculation with output, and reads the fermi level from it."
@@ -619,7 +619,7 @@ function pdos(job, atsym, filter_word="")
     magnetic = ismagneticcalc(scfcalc) 
 
     if package(projwfc) == QE 
-        files = filter(x->occursin("($atsym",x) && occursin("#", x) && occursin(filter_word, x), find_files(job, "pdos"))
+        files = filter(x->occursin("($atsym",x) && occursin("#", x) && occursin(filter_word, x), searchdir(job, "pdos"))
         if isempty(files) 
             @error "No pdos files found in jobdir" 
         end 

src/qe/fileio.jl

@@ -86,7 +86,8 @@ function qe_read_output(filename::String, T=Float64)
             elseif occursin("Fermi", line)
                 out[:fermi]        = parse(T, split(line)[5])
             elseif occursin("lowest unoccupied", line) && occursin("highest occupied", line)
-                out[:fermi]        = parse(T, split(line)[7])
+                sline = split(line)
+                out[:fermi]        = (parse(T, sline[7]) + parse(T, sline[8]))/2
 
             elseif occursin("total energy", line) && line[1] == '!'
                 out[:total_energy]        = parse(T, split(line)[5])

test/job_control_tests.jl

@@ -3,7 +3,6 @@ using DFControl, Test
 testjobpath = joinpath(testdir, "testassets", "test_job")
 
 job = DFJob(testjobpath);
-@test deepcopy(job["scf"]) == job["scf"]
 job4 = DFJob(testjobpath)
 
 #output stuff
@@ -245,7 +244,7 @@ scale_bondlength!(at, at2, 0.5, c)
 @test isapprox((position_cart(at) + position_cart(at2))/2, mid)
 @test isapprox(distance(at, at2), bondlength/2) 
 
-@test isapprox(bandgap(job), 3.6522999999999994)
+@test isapprox(bandgap(job), 2.6701999999999995)
 
 t = job["nscf"]
 curlen = length(job.inputs)
@@ -281,14 +280,14 @@ orig_projs = projections(atoms(job, :Pt)[1])
 job.structure = create_supercell(structure(job), 1, 0, 0, make_afm=true)
 
 DFControl.sanitize_magnetization!(job)
+@test length(atoms(job, :Pt)) == prevlen_Pt
 @test length(atoms(job, :Pt1)) == prevlen_Pt
-@test length(atoms(job, :Pt2)) == prevlen_Pt
 
-@test magnetization(atoms(job, :Pt1)[1]) == [0, 0, 1]
-@test magnetization(atoms(job, :Pt2)[1]) == [0, 0, -1]
+@test magnetization(atoms(job, :Pt)[1]) == [0, 0, 1]
+@test magnetization(atoms(job, :Pt1)[1]) == [0, 0, -1]
 
 DFControl.sanitize_projections!(job)
-@test projections(atoms(job, :Pt1)[1]) != projections(atoms(job, :Pt2)[1])
+@test projections(atoms(job, :Pt)[1]) != projections(atoms(job, :Pt1)[1])
 
 job4.server_dir = "/tmp"
 save(job4)