From 233133c479622fd561a95ec6a16ee6b75e98c200 Mon Sep 17 00:00:00 2001
From: Louis Ponet <louisponet@gmail.com>
Date: Wed, 9 Aug 2023 10:41:33 +0200
Subject: [PATCH] some patches and bugfixes

---
 src/Calculations/qe.jl | 10 +++++++---
 src/Client/job.jl      |  4 ++--
 src/FileIO/qe.jl       | 19 ++++++++++++++-----
 src/FileIO/wannier.jl  |  2 +-
 4 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/src/Calculations/qe.jl b/src/Calculations/qe.jl
index a94a4140..e2e02680 100644
--- a/src/Calculations/qe.jl
+++ b/src/Calculations/qe.jl
@@ -186,7 +186,7 @@ end
 
 function outfiles(c::Calculation{QE})
     files = [c.outfile]
-    for (is, fuzzies) in zip(("projwfc.x", "hp.x"), (("pdos",), ("Hubbard_parameters",)))
+    for (is, fuzzies) in zip(("projwfc.x", "hp.x", "pp.x"), (("pdos",), ("Hubbard_parameters",), ("filplot", "fileout")))
         if c.exec.exec == is
             append!(files, fuzzies)
         end
@@ -337,13 +337,17 @@ function gencalc_projwfc(template::Calculation{QE}, Emin, Emax, DeltaE, extrafla
     end
     tdegaussflag = get(template, :degauss, nothing)
     degauss = tdegaussflag !== nothing ? tdegaussflag : 0.0
-    exec = Exec(path=joinpath(dirname(template.exec.path), "projwfc.x"), modules = deepcopy(template.exec.modules), flags = deepcopy(template.exec.flags))
-    empty!(exec.flags)
+    exec = Exec(path=joinpath(dirname(template.exec), "projwfc.x"), modules = deepcopy(template.exec.modules))
+    
     out = Calculation(deepcopy(template); name = name, exec = exec, data = InputData[])
+    
     set_name!(out, "projwfc")
+    
     empty!(out.flags)
+    
     set_flags!(out, :Emin => Emin, :Emax => Emax, :DeltaE => DeltaE, :ngauss => ngauss,
                :degauss => degauss; print = false)
+                
     set_flags!(out, extraflags...)
     return out
 end
diff --git a/src/Client/job.jl b/src/Client/job.jl
index 5ee38101..d48bc075 100644
--- a/src/Client/job.jl
+++ b/src/Client/job.jl
@@ -386,7 +386,7 @@ function outputdata(job::Job; calcs=map(x->x.name, job.calculations), extra_pars
                     end
                 end
             catch e
-                @warn "Error while reading output of calculation: $(c)\n" e
+                @warn "Error while reading output of calculation: $(c)\n" showerror(stdout, e,stacktrace(catch_backtrace()))
             end
         end
     end
@@ -413,7 +413,7 @@ function bandgap(job::Job, nelec = nothing, outdat = outputdata(job))
         if isempty(n_calcs)
             error("No valid calculation found to extract the number of electrons.\nPlease supply nelec manually.")
         end
-        nelec = maximum(x->get(get(outdat, x.name, Dict()), :fermi, -Inf), n_calcs)
+        nelec = maximum(x->get(get(outdat, x.name, Dict()), :n_electrons, 0), n_calcs)
     end
 
     bands = map(x->outdat[x.name][:bands], filter(x -> haskey(outdat, x.name), band_calcs))
diff --git a/src/FileIO/qe.jl b/src/FileIO/qe.jl
index 4772b54c..e2237fff 100644
--- a/src/FileIO/qe.jl
+++ b/src/FileIO/qe.jl
@@ -716,9 +716,10 @@ function qe_parse_projwfc_output(files...)
 end
 
 function pdos(files, kresolved=false)
-   
     dir = splitdir(files[1])[1]
-    atsyms = Symbol.(unique(map(x -> x[findfirst("(", x)[1]+1:findfirst(")", x)[1]-1],files)))
+    atfiles = filter(x -> occursin("atm", x), files)
+    
+    atsyms = Symbol.(unique(map(x -> x[findfirst("(", x)[1]+1:findfirst(")", x)[1]-1], atfiles)))
     magnetic = (x->occursin("ldosup",x) && occursin("ldosdw",x))(readline(files[1]))
     soc = occursin(".5", files[1])
     files = joinpath.((dir,), files)
@@ -1287,8 +1288,8 @@ end
 
 Writes a string represenation to `f`.
 """
-function Base.write(f::IO, calculation::Calculation{QE}, structure)
-    cursize = f.size
+function Base.write(f::IO, calculation::Calculation{QE}, structure=nothing)
+    cursize = f isa IOBuffer ? f.size : 0
     if Calculations.hasflag(calculation, :calculation)
         Calculations.set_flags!(calculation,
                                 :calculation => replace(calculation[:calculation],
@@ -1312,13 +1313,20 @@ function Base.write(f::IO, calculation::Calculation{QE}, structure)
                 # write(f,"  A = $A\n")
                 write(f, "  nat = $nat\n")
                 write(f, "  ntyp = $ntyp\n")
+            elseif name == :projwfc
+                prefix = calculation[:prefix]
+                outdir = calculation[:outdir]
+                write(f, "  prefix = $prefix\n")
+                write(f, "  outdir = $outdir\n")
             end
+            
             map(writeflag, [(flag, data) for (flag, data) in flags])
             write(f, "/\n\n")
         end
     end
 
     if exec(calculation.exec) == "pw.x"
+        @assert structure !== nothing "Supply a structure to write pw.x input"
         write_structure(f, calculation, structure)
     end
     for dat in calculation.data
@@ -1343,8 +1351,9 @@ function Base.write(f::IO, calculation::Calculation{QE}, structure)
     delete!.((calculation,),
              (:Hubbard_U, :Hubbard_J0, :Hubbard_J, :Hubbard_alpha, :Hubbard_beta,
               :starting_magnetization, :angle1, :angle2, :pseudo_dir))
-    return f.size - cursize
+    return f isa IOBuffer ? f.size - cursize : 0
 end
+
 function Base.write(f::AbstractString, c::Calculation{QE}, structure)
     open(f, "w") do file
         write(file, c, structure)
diff --git a/src/FileIO/wannier.jl b/src/FileIO/wannier.jl
index d8f02887..bdcbf2b0 100644
--- a/src/FileIO/wannier.jl
+++ b/src/FileIO/wannier.jl
@@ -116,7 +116,7 @@ function wan_parse_calculation(file)
                     else
                         m = match(r"\b([\w\d]+):", line)
                         atom        = Symbol(m.captures[1])
-                        projections = map(x->x.captures[1], eachmatch(r"[\s,;]([\w\d]+)", line))
+                        projections = map(x->x.captures[1], eachmatch(r"[:\s,;]([\w\d]+)", line))
                         push!(proj_dict, (atom, projections))
                     end
                     i += 1