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printing update and additional vcrelax and hubbard parsing
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@louisponet
louisponet committed Jun 23, 2021
1 parent a58568e commit 2e2f3a4
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Showing 3 changed files with 99 additions and 27 deletions.
30 changes: 20 additions & 10 deletions src/display/overloads.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ function show(io::IO, block::InputData)
Block data:
"""
dfprintln(io, s)
return dfprintln(io, string(block.data) * "\n\n")
dfprintln(io, string(block.data) * "\n\n")
return
end

show(io::IO, data::Vector{InputData}) = map(x -> show(io, x), data)
Expand All @@ -25,7 +26,8 @@ function show(io::IO, band::DFBand{T}) where {T<:AbstractFloat}
string *= """eigvals: $(band.eigvals[1]) -> $(band.eigvals[end])
extra: $(band.extra)
"""
return dfprintln(io, string)
dfprintln(io, string)
return
end

show(io::IO, bands::Vector{<:DFBand}) = map(x -> show(io, x), bands)
Expand Down Expand Up @@ -81,15 +83,15 @@ function show(io::IO, job::DFJob)
dfprintln(io, crayon"cyan", line, reset)
dfprintln(io, reset, "(", crayon"green", "scheduled", reset, ", ", crayon"red",
"not scheduled", reset, ")")
dfprintln(io)
ln = maximum(length.(string.(name.(is))))
for (si, i) in enumerate(is)
n = name(i)
cr = i.run ? crayon"green" : crayon"red"
dfprint(io, cr, i == last ? (is_running ? "\t$n <- running\n" : "\t$n <- ran last\n") : "\t$n\n")
end
end
return dfprint(io, reset)
dfprint(io, reset)
return
end

function show(io::IO, in::DFCalculation)
Expand All @@ -113,14 +115,16 @@ function show(io::IO, in::DFCalculation)
"$v\n")
end
end
return dfprint(io, crayon"reset")
dfprint(io, crayon"reset")
return
end

function show(io::IO, flag_info::QEFlagInfo{T}) where {T}
df_show_type(io, flag_info)
dfprintln(io, crayon"yellow", "name : $(flag_info.name)")
dfprintln(io, crayon"cyan", "description:", crayon"reset")
return dfprint(io, "\t" * replace(flag_info.description, "\n" => "\n\t"))
dfprint(io, "\t" * replace(flag_info.description, "\n" => "\n\t"))
return
end

function show(io::IO, flag_info::ElkFlagInfo{T}) where {T}
Expand All @@ -133,7 +137,8 @@ function show(io::IO, flag_info::ElkFlagInfo{T}) where {T}
dfprintln(io, "\t" * "nothing")
end
dfprintln(io, crayon"cyan", "description:", crayon"reset")
return dfprintln(io, "\t" * replace(flag_info.description, "\n" => "\n\t"))
dfprintln(io, "\t" * replace(flag_info.description, "\n" => "\n\t"))
return
end

function show(io::IO, info::ElkControlBlockInfo)
Expand All @@ -143,17 +148,20 @@ function show(io::IO, info::ElkControlBlockInfo)
dfprintln(io, "\t$(flag.name)")
end
dfprintln(io, crayon"cyan", "description:", crayon"reset")
return dfprintln(io, "\t" * replace(info.description, "\n" => "\n\t"))
dfprintln(io, "\t" * replace(info.description, "\n" => "\n\t"))
dfprint(io, crayon"reset")
return
end

function show(io::IO, el::Element)
for f in fieldnames(typeof(el))
dfprintln(io, crayon"red", "$f: ", crayon"reset", "$(getfield(el, f))")
end
dfprint(io, crayon"reset")
end

function show(io::IO, str::AbstractStructure)
dfprintln(io, crayon"cyan", "Structure")
dfprintln(io, crayon"cyan", "Structure", crayon"reset")
dfprintln(io, crayon"red", " cell parameters:")
dfprint(io, crayon"reset",
"\t a = $((str.cell[:,1]...,))\n\t b = $((str.cell[:,2]...,))\n\t c = $((str.cell[:,3]...,))\n")
Expand All @@ -162,6 +170,7 @@ function show(io::IO, str::AbstractStructure)
for a in atoms(str)
show(io, a)
end
dfprintln(io, crayon"reset")
end

function show(io::IO, at::AbstractAtom{T,LT}) where {T,LT<:Length{T}}
Expand All @@ -183,5 +192,6 @@ function show(io::IO, at::AbstractAtom{T,LT}) where {T,LT<:Length{T}}
dfprint(io, "$f: $val, ")
end
end
return dfprintln(io)
dfprintln(io, crayon"reset")
return
end
94 changes: 78 additions & 16 deletions src/qe/fileio.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,45 @@ function qe_read_output(calculation::DFCalculation{QE}, args...; kwargs...)
end
end

function parse_Hubbard_block(f)
# Each of these will have n Hubbard typ elements at the end
ids = Int[]
traces = NamedTuple{(:up, :down, :total), NTuple{3, Float64}}[]
eigvals = (up = Vector{Float64}[], down = Vector{Float64}[])
eigvec = (up = Matrix{Float64}[], down=Matrix{Float64}[])
occupations = (up = Matrix{Float64}[], down=Matrix{Float64}[])
magmoms = Float64[]
line = readline(f)
cur_spin = :up
while strip(line) != "--- exit write_ns ---"
line = readline(f)
if line[1:4] == "atom"
sline = split(line)
push!(ids, parse(Int, sline[2]))
push!(traces, NamedTuple{(:up, :down, :total)}(parse.(Float64, (sline[end-2], sline[end-1], sline[end]))))
for spin in (:up, :down)
readline(f) #should be spin1
readline(f)# should be eigvals
push!(eigvals[spin], parse.(Float64, split(readline(f))))
dim = length(eigvals[spin][1])
readline(f) #eigvectors
tmat = zeros(dim, dim)
for i = 1:dim
tmat[i, :] = parse.(Float64, split(readline(f)))
end
push!(eigvec[spin], tmat)
readline(f) #occupations
for i = 1:dim
tmat[i, :] = parse.(Float64, split(readline(f)))
end
push!(occupations[spin], tmat)
end
push!(magmoms, parse(Float64, split(readline(f))[end]))
end
end
return [(id = i, trace = t, eigvals = (up = val_up, down = val_down), eigvecs = (up = vec_up, down=vec_down), occupations = (up=occ_up, down=occ_down), magmom = m) for (i, t, val_up,val_down, vec_up,vec_down, occ_up,occ_down, m) in zip(ids, traces, eigvals.up,eigvals.down, eigvec.up,eigvec.down, occupations.up,occupations.down, magmoms)]
end

"""
qe_read_pw_output(filename::String, T=Float64)
Expand All @@ -58,7 +97,10 @@ function qe_read_pw_output(filename::String, T = Float64; cleanup = true)
atsyms = Symbol[]
nat = 0
while !eof(f)
line = readline(f)
line = strip(readline(f))
if isempty(line)
continue
end
#polarization
if occursin("C/m^2", line)
s_line = split(line)
Expand Down Expand Up @@ -211,11 +253,29 @@ function qe_read_pw_output(filename::String, T = Float64; cleanup = true)
end
out[:atomic_positions] = atoms
elseif occursin("Total force", line)
force = parse(T, split(line)[4])
if force <= lowest_force
lowest_force = force
out[:total_force] = force
sline = split(line)
force = parse(T, sline[4])
scf_contrib = parse(T, sline[end])
if !haskey(out, :total_force)
out[:total_force] = [force]
else
push!(out[:total_force], force)
end
if !haskey(out, :scf_correction)
out[:scf_correction] = [scf_contrib]
else
push!(out[:scf_correction], scf_contrib)
end
elseif occursin("iteration #", line)
sline = split(line)
it = length(sline[2]) == 1 ? parse(Int, sline[3]) : parse(Int, sline[2][2:end])
if !haskey(out, :scf_iteration)
out[:scf_iteration] = [it]
else
push!(out[:scf_iteration], it)
end


elseif occursin("Magnetic moment per site", line)
key = :colin_mag_moments
out[key] = T[]
Expand All @@ -241,8 +301,10 @@ function qe_read_pw_output(filename::String, T = Float64; cleanup = true)
out[key] = [mag]
end
elseif occursin("convergence NOT achieved", line)
out[:converged] = false
out[:scf_converged] = false
elseif occursin("convergence has been achieved", line)
out[:scf_converged] = true
elseif occursin("Begin final coordinates", line)
out[:converged] = true
elseif occursin("atom number", line)
if !haskey(out, :magnetization)
Expand All @@ -257,16 +319,12 @@ function qe_read_pw_output(filename::String, T = Float64; cleanup = true)
out[:magnetization][atom_number] = parse(Vec3{Float64},
split(readline(f))[3:5])
end
elseif occursin("Tr[ns(na)]", line)
if !haskey(out, :Hubbard_occupation)
out[:Hubbard_occupation] = Float64[]
end
sline = split(line)
id = parse(Int, split(line)[2])
if length(out[:Hubbard_occupation]) < id
push!(out[:Hubbard_occupation], parse(Float64, sline[end]))
elseif line == "--- enter write_ns ---"

if !haskey(out, :Hubbard)
out[:Hubbard] = [parse_Hubbard_block(f)]
else
out[:Hubbard_occupation][id] = parse(Float64, sline[end])
push!(out[:Hubbard], parse_Hubbard_block(f))
end
# Timing info
elseif occursin("init_run", line)
Expand Down Expand Up @@ -384,7 +442,11 @@ function qe_read_pw_output(filename::String, T = Float64; cleanup = true)
pop!(out, f, nothing)
end
end

out[:converged] = out[:converged] ? true : haskey(out, :scf_converged) && out[:scf_converged] && !haskey(out, :total_force)
if haskey(out, :scf_iteration)
out[:n_scf] = length(findall(i -> out[:scf_iteration][i+1] < out[:scf_iteration][i], 1:length(out[:scf_iteration])-1))
end
pop!(out, :scf_converged, nothing)
return out
end
end
Expand Down
2 changes: 1 addition & 1 deletion test/testassets/test_job/nscf.in
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
verbosity = 'high'
calculation = 'nscf'
outdir = 'localhost/test_job/outputs'
pseudo_dir = '/home/ponet/.julia/dev/DFControl/test/testassets/test_job'
pseudo_dir = '/home/lponet/.julia/dev/DFControl/test/testassets/test_job'
restart_mode = 'from_scratch'
/

Expand Down

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