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cleanup + Hubbard + outputs copy
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@louisponet
louisponet committed Jun 12, 2021
1 parent 83394d9 commit 61cb44c
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Showing 11 changed files with 242 additions and 228 deletions.
7 changes: 7 additions & 0 deletions src/elk/input.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
infilename(input::DFInput{Elk}) = "elk.in"

isbandscalc(input::DFInput{Elk}) = input.name == "20"

isnscfcalc(input::DFInput{Elk}) = input.name == "elk2wannier" #nscf == elk2wan??

isscfcalc(input::DFInput{Elk}) = input.name ∈ ["0", "1"]
197 changes: 12 additions & 185 deletions src/input.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,6 @@ flags(input::DFInput) = input.flags
set_dir!(input::DFInput, dir) = (input.dir = dir)
name_ext(input::DFInput, ext) = name(input) * ext
infilename(input::DFInput) = input.infile
infilename(input::DFInput{Elk}) = "elk.in"
outfilename(input::DFInput) = input.outfile
inpath(input::DFInput) = joinpath(input, infilename(input))
outpath(input::DFInput) = joinpath(input, outfilename(input))
Expand All @@ -86,7 +85,7 @@ hasexec(input::DFInput, ex::AbstractString) = exec(input, ex) != nothing
set_flow!(input::DFInput, run) = input.run = run

"Runs through all the set flags and checks if they are allowed and set to the correct value"
function cleanflags!(input::DFInput)
function convert_flags!(input::DFInput)
for (flag, value) in flags(input)
flagtype_ = flagtype(input, flag)
if flagtype_ == Nothing
Expand Down Expand Up @@ -114,30 +113,16 @@ end

#TODO implement abinit and wannier90
"""
sanitizeflags!(input::DFInput)
sanitize_flags!(input::DFInput, str::AbstractStructure)
Cleans up flags, i.e. remove flags that are not allowed and convert all
flags to the correct types.
Tries to correct common errors for different input types.
"""
function sanitizeflags!(input::DFInput)
cleanflags!(input)
function sanitize_flags!(input::DFInput, str::AbstractStructure)
convert_flags!(input)
end

function sanitizeflags!(input::DFInput{QE})
cleanflags!(input)
if isvcrelaxcalc(input)
#this is to make sure &ions and &cell are there in the input
!hasflag(input, :ion_dynamics) && set_flags!(input, :ion_dynamics => "bfgs", print=false)
!hasflag(input, :cell_dynamics) && set_flags!(input, :cell_dynamics => "bfgs", print=false)
end
#TODO add all the required flags
if exec(input, "pw.x") !== nothing
@assert hasflag(input, :calculation) "Please set the flag for calculation with name: $(name(input))"
end
end


function setoradd!(datas::Vector{InputData}, data::InputData)
found = false
for (i, d) in enumerate(datas)
Expand All @@ -162,29 +147,14 @@ function set_data!(input::DFInput, data::InputData)
return input
end

isbandscalc(input::DFInput{QE}) = flag(input, :calculation) == "bands"
isbandscalc(input::DFInput{Elk}) = input.name == "20"
isbandscalc(input::DFInput) = false

isnscfcalc(input::DFInput{QE}) = flag(input, :calculation) == "nscf"
isnscfcalc(input::DFInput{Elk}) = input.name == "elk2wannier" #nscf == elk2wan??
isnscfcalc(input::DFInput) = false

isscfcalc(input::DFInput{QE}) = flag(input, :calculation) == "scf"
isscfcalc(input::DFInput{Elk}) = input.name ∈ ["0", "1"]
isscfcalc(input::DFInput) = false

isvcrelaxcalc(input::DFInput{QE}) = flag(input, :calculation) == "vc-relax"
isvcrelaxcalc(input::DFInput) = false

isprojwfccalc(input::DFInput{QE}) = hasexec(input, "projwfc.x")
isprojwfccalc(input::DFInput) = false

issoccalc(input::DFInput{QE}) = flag(input, :lspinorb) == true
issoccalc(input::DFInput{Wannier90}) = flag(input, :spinors) == true
issoccalc(input::DFInput) = false

ishpcalc(input::DFInput{QE}) = hasexec(input, "hp.x")

#TODO review this!
outdata(input::DFInput) = input.outdata
Expand All @@ -193,62 +163,7 @@ hasoutput(input::DFInput) = !isempty(outdata(input)) || hasoutfile(input)
hasoutfile(input::DFInput) = ispath(outpath(input))
hasnewout(input::DFInput, time) = mtime(outpath(input)) > time

readoutput(input::DFInput{QE}) = qe_read_output(input)
readoutput(input::DFInput{Wannier90}) = wan_read_output(outpath(input))

pseudodir(input::DFInput{QE}) = flag(input, :pseudo_dir)

set_cutoffs!(input::DFInput, args...) = @warn "Setting cutoffs is not implemented for package $(package(input))"
set_cutoffs!(input::DFInput{QE}, ecutwfc, ecutrho) = set_flags!(input, :ecutwfc => ecutwfc, :ecutrho=>ecutrho)

function Emin_from_projwfc(structure::AbstractStructure, projwfc::DFInput{QE}, threshold::Number)
hasoutput_assert(projwfc)
hasexec_assert(projwfc, "projwfc.x")
if !haskey(outdata(projwfc), :states)
states, bands = qe_read_projwfc(outpath(projwfc))
outdata(projwfc)[:states] = states
outdata(projwfc)[:bands] = bands
else
states, bands = outdata(projwfc)[:states], outdata(projwfc)[:bands]
end

mask = zeros(length(states))
for (atid, at) in enumerate(atoms(structure))
projs = projections(at)

if isempty(projs)
continue
end

stateids = Int[]
for proj in projs
orb = orbital(proj)
push!.((stateids,), findall(x -> x.atom_id == atid && x.l == orb.l, states))
end
mask[stateids] .= 1.0

end
Emin = -10000.0
for b in bands
ψ = mean(b.extra[:ψ])
tot_relevant_occupation = dot(mask, ψ)

if tot_relevant_occupation > threshold
Emin = minimum(b.eigvals)
break
end

end
if Emin == -10000.0
error("Couldn't find any band with occupation of relevant projections above $threshold, were any set in the structure?")
end
return Emin
end

#asserts
function iscalc_assert(i::DFInput{QE}, calc)
@assert flag(i, :calculation) == calc "Please provide a valid '$calc' calculation."
end

function hasoutput_assert(i::DFInput)
@assert hasoutfile(i) "Please specify an input that has an outputfile."
Expand All @@ -258,106 +173,18 @@ function hasexec_assert(i::DFInput, exec::String)
@assert hasexec(i, exec) "Please specify an input with $exec as it's executable."
end


#TODO Temporary handling of HubbardU situation
function set_hubbard_flags!(input::DFInput{QE}, str::AbstractStructure{T}) where {T}
u_ats = unique(atoms(str))
isdftucalc = any(x -> dftu(x).U != 0 || dftu(x).J0 != 0.0 || sum(dftu(x).J) != 0 || sum(dftu(x).α) != 0, u_ats)
isnc = isnoncolin(str)
if isdftucalc
Jmap = map(x -> copy(dftu(x).J), u_ats)
Jdim = maximum(length.(Jmap))
Jarr = zeros(Jdim, length(u_ats))
for (i, J) in enumerate(Jmap)
diff = Jdim - length(J)
if diff > 0
for d in 1:diff
push!(J, zero(eltype(J)))
end
end
Jarr[:, i] .= J
end
set_flags!(input,
:lda_plus_u => true,
:Hubbard_U => map(x -> dftu(x).U, u_ats),
:Hubbard_alpha => map(x -> dftu(x).α , u_ats),
:Hubbard_beta => map(x -> dftu(x).β , u_ats),
:Hubbard_J => Jarr,
:Hubbard_J0 => map(x -> dftu(x).J0, u_ats);
print=false)
isnc && set_flags!(input, :lda_plus_u_kind => 1; print=false)
end
end

function set_starting_magnetization_flags!(input::DFInput{QE}, str::AbstractStructure{T}) where {T}
u_ats = unique(atoms(str))
mags = magnetization.(u_ats)
starts= T[]
θs = T[]
ϕs = T[]
ismagcalc = ismagnetic(str)
isnc = isnoncolin(str)
if (ismagcalc && isnc) || (flag(input, :noncolin) !== nothing && flag(input, :noncolin))
for m in mags
tm = normalize(m)
if norm(m) == 0
push!.((starts, θs, ϕs), 0.0)
else
θ = acos(tm[3]) * 180/π
ϕ = atan(tm[2], tm[1]) * 180/π
start = norm(m)
push!(θs, θ)
push!(ϕs, ϕ)
push!(starts, start)
end
end
set_flags!(input, :noncolin => true; print=false)
rm_flags!(input, :nspin; print=false)
elseif ismagcalc
for m in mags
push!.((θs, ϕs), 0.0)
if norm(m) == 0
push!(starts, 0)
else
push!(starts, sign(sum(m))*norm(m))
end
end
set_flags!(input, :nspin => 2; print=false)
end
set_flags!(input, :starting_magnetization => starts, :angle1 => θs, :angle2 => ϕs; print=false)
end

Base.:(==)(i1::DFInput, i2::DFInput) =
all(x -> x == :outdata ? true : getfield(i1, x) == getfield(i2, x), fieldnames(DFInput))

searchdir(i::DFInput, glob) = joinpath.((i,), searchdir(dir(i), glob))

for f in (:cp, :mv)
@eval function Base.$f(i::DFInput{QE}, dest::String; kwargs...)
$f(inpath(i), joinpath(dest, infilename(i)); kwargs...)
if hasoutfile(i)
$f(outpath(i), joinpath(dest, outfilename(i)); kwargs...)
end
if isprojwfccalc(i)
for f in searchdir(i, "pdos")
$f(f, joinpath(dest, splitdir(f)[end]); kwargs...)
end
elseif ishpcalc(i)
for f in searchdir(i, "Hubbard_parameters")
$f(f, joinpath(dest, splitdir(f)[end]); kwargs...)
end
end
#TODO add ph.x outfiles
end

@eval function Base.$f(i::DFInput{Wannier90}, dest::String; kwargs...)
for glob in ("$(name(i))", "UNK") # seedname should also cover generated pw2wannier90 files
for f in searchdir(i, glob)
$f(f, joinpath(dest, splitdir(f)[end]); kwargs...)
end
end
end
end

ψ_cutoff_flag(::DFInput{P}) where {P} = ψ_cutoff_flag(P)
ρ_cutoff_flag(::DFInput{P}) where {P} = ρ_cutoff_flag(P)


include("qe/input.jl")
include("elk/input.jl")
include("wannier90/input.jl")



18 changes: 9 additions & 9 deletions src/job.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,9 @@ Represents a full DFT job with multiple input files and calculations.
server_dir ::String = ""
header ::Vector{String} = getdefault_jobheader()
metadata ::Dict = Dict()
version ::Int = last_job_version(local_dir)
function DFJob(name, structure, calculations, local_dir, server, server_dir, header, metadata, version)
version ::Int = last_job_version(local_dir)
copy_temp_folders::Bool = true
function DFJob(name, structure, calculations, local_dir, server, server_dir, header, metadata, version, copy_temp_folders)
if local_dir[end] == '/'
local_dir = local_dir[1:end-1]
end
Expand All @@ -31,7 +32,7 @@ Represents a full DFT job with multiple input files and calculations.
metadata = load(mpath)
end
end
out = new(name, structure, calculations, local_dir, server, server_dir, header, metadata, version)
out = new(name, structure, calculations, local_dir, server, server_dir, header, metadata, version, copy_temp_folders)
# TODO add check_version, and if it doesn't match the one that's currently in the main directory,
# load the previous one from the versions
!occursin("versions", local_dir) && maybe_register_job(local_dir)
Expand Down Expand Up @@ -126,7 +127,7 @@ inpath(job::DFJob, n) = inpath(input(job,n))
outpath(job::DFJob, n) = outpath(input(job,n))

"Runs some checks on the set flags for the inputs in the job, and sets metadata (:prefix, :outdir etc) related flags to the correct ones. It also checks whether flags in the various inputs are allowed and set to the correct types."
function sanitizeflags!(job::DFJob)
function sanitize_flags!(job::DFJob)
set_flags!(job, :prefix => "$(job.name)", print=false)
if iswannierjob(job)
nscfcalc = getnscfcalc(job)
Expand All @@ -146,9 +147,7 @@ function sanitizeflags!(job::DFJob)
outdir = isempty(job.server_dir) ? joinpath(job, "outputs") : joinpath(job.server_dir, splitdir(job.local_dir)[end], "outputs")
set_flags!(i, :outdir => "$outdir", print=false)
end
sanitize_cutoffs!(job)
sanitize_pseudos!(job)
sanitizeflags!.(inputs(job))
sanitize_flags!.(inputs(job), (job.structure,))
end

function sanitize_cutoffs!(job)
Expand Down Expand Up @@ -179,6 +178,7 @@ function sanitize_pseudos!(job::DFJob)
all_pseudos = pseudo.(atoms(job))
uni_dirs = unique(map(x->x.dir, all_pseudos))
uni_pseudos = unique(all_pseudos)
@assert all(ispath.(path.(uni_pseudos))) "Some Pseudos could not be found, please set them to existing ones."
pseudo_dir = length(uni_dirs) == 1 ? uni_dirs[1] : job.local_dir
if length(uni_dirs) > 1
@info "Found pseudos in multiple directories, copying them to job directory"
Expand All @@ -192,7 +192,7 @@ function sanitize_pseudos!(job::DFJob)
end

function sanitize_magnetization!(job::DFJob)
if !any(x->package(x) == QE, inputs(job))
if !any(x -> package(x) == QE, inputs(job))
return
end
sanitize_magnetization!(job.structure)
Expand Down Expand Up @@ -266,7 +266,7 @@ for f in (:cp, :mv)
@eval function Base.$f(job::DFJob, dest::String; kwargs...)
tjob = DFJob(job.local_dir)
for file in readdir(job.local_dir)
if file == VERSION_DIR_NAME
if file == VERSION_DIR_NAME || (file == "outputs" && !job.copy_temp_folders)
continue
end
$f(joinpath(tjob, file), joinpath(dest, file); kwargs...)
Expand Down
4 changes: 3 additions & 1 deletion src/jobAPI.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,11 @@ function save(job::DFJob, local_dir=job.local_dir; kwargs...)
end
maybe_register_job(job)
maybe_increment_version(job)
sanitize_cutoffs!(job)
sanitize_pseudos!(job)
sanitize_magnetization!(job)
sanitize_projections!(job)
sanitizeflags!(job)
sanitize_flags!(job)
return writejobfiles(job; kwargs...)
end

Expand Down
1 change: 1 addition & 0 deletions src/qe/constants.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -150,3 +150,4 @@ flagtype(::Type{QE}, exec, flag) = eltype(qe_flaginfo(exec, flag))
ψ_cutoff_flag(::Type{QE}) = :ecutwfc
ρ_cutoff_flag(::Type{QE}) = :ecutrho


8 changes: 0 additions & 8 deletions src/qe/fileio.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -893,14 +893,6 @@ function save(input::DFInput{QE}, structure, filename::String=inpath(input); rel
if haskey(flags(input), :calculation)
set_flags!(input, :calculation => replace(input[:calculation], "_" => "-"), print=false)
end
# setting hubbard and magnetization flags
set_hubbard_flags!(input, structure)
set_starting_magnetization_flags!(input, structure)

# setting hubbard flags
pseudo_dir = pseudo(atoms(structure)[1]).dir # Pseudos should be all sanitized by now
set_flags!(input, :pseudo_dir => pseudo_dir; print=false)

open(filename, "w") do f
if exec(input, "ph.x") !== nothing
write(f, "--\n")
Expand Down
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