Fixes and Examples

examples/1createandrun_job_from_cif.jl

@@ -0,0 +1,84 @@
+#This example requires cif2cell to be installed, and have it set in your PATH.
+using DFControl
+
+#This example goes through how one would create a job from scratch, using a .cif file for the Structure.
+
+#First go to your favourite Crystal structure database and download the .cif you want to use.
+#e.g. Si (F d -3 m :1) : http://www.crystallography.net/cod/9011998.cif
+
+#We want to run an 'scf' and 'bands' calculation using QuantumEspresso.
+
+
+#Variables that will be passed to the `DFJob` constructor.
+
+name = "Si" #this name will also be given to the Structure inside the DFJob
+local_dir = "/home/ponet/Documents/Si"
+server_dir = "/home/ponet/Si"
+run_command = "mpirun -np 24"
+bin_dir = "/usr/local/bin" #this is defaulted to the users bin dir = "~/bin/", it is the directory where pw.x etc will be called from
+
+pseudo_set = :pbesol #nonrelativistic calculation ( assumes you set up the pseudos, as demonstrated in the README)
+pseudo_specifier = "paw" #this selects the correct pseudo if multiple belong to the pseudo_set. If you don't specify this, the first one in the set will be used.
+
+#The header holds all the other information inside a job scriptfile that is not recognized as input and output.
+header = ["#SBATCH -N 1", "#SBATCH --ntasks-per-node=24",
+          "#SBATCH --time=24:00:00", "#SBATCH -p defpart",
+          "module load open-mpi/gcc/1.10.4-hfi", "module load mkl/2016.1.056"
+         ]
+
+#The various calculations we want to run and the flags and data to pass to them are defined in two ways:
+#   - calculation specific flags and data are associated with the calculation they belong to
+#   - common flags can be defined as Pair{Symbol, Any} varargs at the end of the constructor call.
+scf_data = Dict(:k_points => (6, 6, 6, 1, 1, 1), :flags => [:verbosity => "'low'"])
+bands_data = Dict(:k_points => [(0.5, 0.5, 0.5, 100.),
+                                (0.0, 0.0, 0.0, 100.),
+                                (0.0, 0.5, 0.0, 1.)],
+                  :flags => [:verbosity => "'high'", :nbnd => 8])
+
+calculations = [:scf => scf_data, :bands => bands_data] #the order here is the order in which the calculations will run!
+
+#Now we load the cif file and create a `DFJob` from it.
+
+job = DFJob(name, local_dir, "/home/ponet/Downloads/9011998.cif", calculations,
+      :prefix       => "'silicon'",
+      :restart_mode => "'from_scratch'",
+      :ecutwfc      => 18.0,
+      :mixing_mode  => "'plain'",
+      :mixing_beta  => 0.7,
+      :conv_thr     => 1.0e-8,
+      #kwargs
+      server_dir  = server_dir,
+      bin_dir     = bin_dir,
+      run_command = run_command,
+      header      = header,
+      pseudo_set  = :pbesol,
+      pseudo_specifier = pseudo_specifier
+     )
+# An additional kwarg is `server=get_default_server()`, which is set to the server you have defined while following the setup in README.
+# This can ofcourse be changed to a different server.
+
+#Now the job can be submitted to the server to run.
+submit_job(job)
+#this first saves the job and it's input files to the `job.local_dir` then pushes the `job.tt` file and the inputs to the `job.server_dir` on `job.server`, and runs the `qsub job.tt` command.
+#You can check the job.local_dir to see the input files and `job.tt` script.
+
+#you can observe the slurm qstat by doing
+qstat()
+#or watch it by
+watch_qstat()
+#these default to run the commands on the default server
+
+#hopefully everything went according to plan and we can watch our outputs
+outputs = pull_outputs(job)
+
+#now the bandstructure can be plotted
+bands = read_qe_output(outputs[2])[:bands]
+#alt:
+bands = read_qe_bands_file(outputs[2])
+
+fermi = read_qe_output(outputs[1])[:fermi]
+#alt:
+fermi = read_fermi_from_qe_output(outputs[1])
+using Plots
+
+plot(bands, fermi=fermi)

examples/2edit_job_resubmit.jl

@@ -0,0 +1,30 @@
+#This example assumes that you ran through the first one.
+# It will show how to load a job from a server, and change flags.
+
+using DFControl
+
+server_dir = "Si/"
+local_dir  = "/home/ponet/Documents/Si"
+job = load_server_job(server_dir, local_dir)
+#shorthand:
+job = ldsj(server_dir, local_dir) #for other shorthands see DFControl/src/shorthands.jl
+
+#change flags
+change_flags!(job, :ecutwfc => 25.0)  #more `Pair{Symbol, Any}`'s can be given as varargs.
+#shorthand: chfls!
+#change_flags! will only go through already set flags to change them,
+#if you want to set new flags simply do (it can also be used to change already set flags):
+
+set_flags!(job, :ecut_rho => 80.) #won't work, it goes through the QE documentation to find the allowed flags for the input files in the job, and also tries to convert the given value to what it should be.
+
+set_flags!(job, :ecutrho => 80., :diagonalization => "'david'")
+#shorthand: stfls!
+
+#now we might not want to run all the calculations again.
+#one can change the job "flow":
+change_flow!(job, "scf" => false) #again, more `Pair{String, Bool}`'s can be given as varargs
+#This looks through all the calculations inside the job, if the `calculation.name` (derived from it's filename) contains a given `String`, it will set `calculation.run` to the corresponding `Bool`.
+#If a job has calculations/inputs that don't need to run, their line will be commented out in `job.tt` script.
+
+#now we can resubmit the job with the changed flags
+sbmj(job)

src/DFControl.jl

@@ -1,4 +1,4 @@
-__precompile__(true)
+__precompile__()
 module DFControl
 # using Reexport
     using RecipesBase
@@ -105,6 +105,7 @@ module DFControl
     export set_default_server
     export configure_default_pseudos
     export remove_default_pseudo_dir
+    export get_default_pseudo
     export set_default_job_header
     export @add_default
     export load_defaults

src/defaults.jl

@@ -122,7 +122,7 @@ function get_default_pseudo_dir(pseudo_set)
 end
 
 """
-    configure_default_pseudos!(server = get_default_server(), pseudo_dirs=get_default_pseudo_dirs())
+    configure_default_pseudos(server = get_default_server(), pseudo_dirs=get_default_pseudo_dirs())
 
 Reads the specified `default_pseudo_dirs` on the `default_server` and sets up the `default_pseudos` variable, and also adds all the entries to the `user_defaults.jl` file.
 """

src/job.jl

@@ -33,41 +33,38 @@ mutable struct DFJob
 end
 
 #TODO implement abinit
-# function DFJob(job_name, local_dir, calculations::Array{Pair{Union{Symbol, String}, Dict},1}, atoms, cell_parameters=eye(3);
-function DFJob(job_name, local_dir, calculations::Vector, structure::AbstractStructure;
+function DFJob(job_name, local_dir, structure::AbstractStructure, calculations::Vector, common_flags...;
                     server=get_default_server(),
                     server_dir="",
                     package=:qe,
                     bin_dir="~/bin/",
                     run_command="mpirun -np 24",
-                    common_flags=Dict{Symbol,Any}(),
                     pseudo_set=:default,
                     pseudo_specifier="",
                     header=get_default_job_header())
 
     @assert package==:qe "Only implemented for Quantum Espresso!"
     local_dir = form_directory(local_dir)
-    job_atoms = convert_2atoms(atoms,pseudo_set=pseudo_set, pseudo_specifier=pseudo_specifier)
     job_calcs = DFInput[]
     if typeof(common_flags) != Dict
         common_flags = Dict(common_flags)
     end
-
+    bin_dir = form_directory(bin_dir)
     req_flags = Dict(:prefix  => "'$job_name'",
                      :outdir => "'$server_dir'",
                      :ecutwfc => 25.)
     merge!(req_flags, common_flags)
     for (calc, data) in calculations
         calc_ = typeof(calc) == String ? Symbol(calc) : calc
         if in(calc_, [Symbol("vc-relax"), :relax, :scf])
-            k_points = pop!(data, :k_points, [1, 1, 1, 0, 0, 0])
+            k_points = get(data, :k_points, [1, 1, 1, 0, 0, 0])
             k_option = :automatic
         elseif calc_ == :nscf
-            k_points = pop!(data, :k_points, (1, 1, 1))
+            k_points = get(data, :k_points, (1, 1, 1))
             k_grid   = gen_k_grid(k_points..., :nscf)
             k_option = :crystal
         elseif calc_ == :bands
-            k_points = pop!(data, :k_points, [0., 0., 0., 1.])
+            k_points = get(data, :k_points, [[0., 0., 0., 1.]])
             num_k = 0.0
             for point in k_points
                 num_k += point[4]
@@ -77,7 +74,7 @@ function DFJob(job_name, local_dir, calculations::Vector, structure::AbstractStr
             end
             k_option = :crystal_b
         end
-        flags  = pop!(data, :flags, Dict{Symbol, Any}())
+        flags  = get(data, :flags, Dict{Symbol, Any}())
         push!(flags, :calculation => "'$(string(calc_))'")
         input_ = QEInput(string(calc_) * ".in",
                          QEControlBlock[],
@@ -87,15 +84,16 @@ function DFJob(job_name, local_dir, calculations::Vector, structure::AbstractStr
                          true)
         set_flags!(input_, req_flags..., print=false)
         set_flags!(input_, flags..., print=false)
-        change_atoms!(input_, job_atoms, pseudo_set = pseudo_set, pseudo_specifier = pseudo_specifier, print=false)
         push!(job_calcs, input_)
     end
+    out = DFJob(job_name, structure, job_calcs, local_dir, server, server_dir, header)
+    change_atoms!(out, structure.atoms, pseudo_set = pseudo_set, pseudo_specifier= pseudo_specifier)
     return DFJob(job_name, structure, job_calcs, local_dir, server, server_dir, header)
 end
 
-function DFJob(job_name, local_dir, calculations::Vector, ciffile::String; kwargs...)
+function DFJob(job_name, local_dir, ciffile::String, calculations::Vector, args...; kwargs...)
     structure = Structure(ciffile, name=job_name)
-    return DFJob(job_name, local_dir, calculations, structure; kwargs...)
+    return DFJob(job_name, local_dir, structure, calculations, args... ; kwargs...)
 end
 
 function DFJob(job::DFJob, flagstoset...;
@@ -279,6 +277,12 @@ function push_job(job::DFJob, newfiles)
     if !ispath(job.local_dir)
         error("Please save the job locally first using save_job(job)!")
     else
+        try
+            run(`ssh -t $(job.server) touch $(job.server_dir * "tmp.in")`)
+            run(`ssh -t $(job.server) rm $(job.server_dir * "tmp.in")`)
+        catch
+            run(`ssh -t $(job.server) mkdir $(job.server_dir)`)
+        end
         for file in newfiles
             run(`scp $(job.local_dir * file) $(job.server * ":" * job.server_dir)`)
         end

src/qe/fileio.jl

@@ -52,9 +52,11 @@ function read_qe_output(filename::String, T=Float64)
                 #fermi energy
             elseif contains(line, "Fermi")
                 out[:fermi]        = parse(T, split(line)[5])
-            elseif contains(line, "lowest unoccupied") || contains(line, "highest occupied")
+            elseif contains(line, "lowest unoccupied") && contains(line, "highest occupied")
                 out[:fermi]        = parse(T, split(line)[7])
 
+            elseif contains(line, "lowest unoccupied") || contains(line, "highest occupied")
+                out[:fermi]        = parse(T, split(line)[5])
                 #setup for k_points
             elseif contains(line, "celldm(1)")
                 alat_bohr = parse(T, split(line)[2])
@@ -148,7 +150,7 @@ function read_qe_output(filename::String, T=Float64)
                 for i = 1:length(out[:k_cart])
                     push!(eig_band, k_eigvals[i][i1])
                 end
-                push!(out[:bands], DFBand(out[:k_cart], out[:k_cryst], eig_band))
+                push!(out[:bands], DFBand(get(out, :k_cart,[[0.0,0.0,0.0]]), get(out, :k_cryst, [[0.0,0.0,0.0]]), eig_band))
             end
         end
         return out
@@ -249,6 +251,21 @@ read_qe_vcrel(filename::String, T=Float64) = read_qe_output(filename, T) do x
 #         return out
 #     end
 # end
+function alat(control_blocks, pop=false)
+    sysblock = block(control_blocks, :system)
+    if sysblock == nothing
+        error("Could not resolve the alat!")
+    end
+    if haskey(sysblock.flags, :A)
+        alat = pop ? pop!(sysblock.flags, :A) : sysblock.flags[:A]
+    elseif haskey(sysblock.flags, celldm_1)
+        alat = pop ? pop!(sysblock.flags, celldm_1) : sysblock.flags[celldm_1]
+        alat *= conversions[:bohr2ang]
+    else
+        error("So far alat can be specified only through A and celldm(1).")
+    end
+    return alat
+end
 
 #TODO handle more fancy cells
 function extract_cell!(control_blocks, cell_block)
@@ -414,14 +431,14 @@ function read_qe_input(filename, T=Float64::Type; exec="pw.x", run_command="", r
 end
 
 function write_block_data(f, data)
-    if typeof(data) <: Array{Vector{Float64},1} || typeof(data) <: Array{Vector{Float64},1} #k_points
+    if typeof(data) <: Vector{Vector{Float64}} || typeof(data) <: Vector{NTuple{4, Float64}} #k_points
         for x in data
             for y in x
                 write(f, " $y")
             end
             write(f, "\n")
         end
-    elseif typeof(data) <: Array{Int,1}
+    elseif typeof(data) <: Vector{Int} || typeof(data) <: NTuple{6, Int}
         for x in data
             write(f, " $x")
         end
@@ -447,8 +464,18 @@ function write_input(input::QEInput, structure, filename::String=input.filename)
         write_flag(flag_data) = write_flag_line(f, flag_data[1], flag_data[2])
         write_block(data)     = write_block_data(f, data)
 
-
-        for block in input.control_blocks
+        blocks2file = QEControlBlock[]
+        c_block = getfirst(x -> x.name == :control, input.control_blocks)
+        s_block = getfirst(x -> x.name == :system, input.control_blocks)
+        if c_block != nothing
+            push!(blocks2file, c_block)
+            push!(blocks2file, s_block)
+        end
+        rest = filter(x -> x.name != :control && x.name != :system, input.control_blocks)
+        for r in rest
+            push!(blocks2file, r)
+        end
+        for block in blocks2file
             write(f, "&$(block.name)\n")
             if block.name == :system
                 nat   = length(structure.atoms)