example.yml

#name this anything you'd like, but this is a nice convention to follow
title: 'AuPt Alloy Database' 
# Ordered list of species; this is the same order as should be in the
# POTCAR file for VASP calculations. You can have 2 or 3
species:
  - 'Au'
  - 'Pt'
# Directory in which the database folder system will be created.
root: '~/AuPt'
# These are global settings for INCAR, POTCAR, and KPOINTS that will
# be applied to *all* the VASP calculations in all databases. They can
# be overridden in each database.
calculator:
  #theres some other software programs we can make input files for with aBuild.
  #You'll probably only need vasp here
  active: 'vasp_and_lammps_and_qe' 
  vasp:
    #If your system of choice has atoms with a non-zero magnetic moment (is ferromagnetic), you should assign it
    #a magmom here. 2 is a good choice. Otherwise comment this section out.
    FM:
      Ag: 2
      Pt: 0
    #in very special cases you might need this AFM section. Otherwise comment it out
    AFM: #if you'd like to make a structure antiferromagnetic, specify the details here
      plane: [1,0,0] #plane to align spin on 
      spin_type: 0 #which atom gets the spin. Remember the species list is in reverse alphabetical order
    #these are the settings that will be written in the INCAR for each vasp calculation. Add extra if you've
    #done some research about it (and probably talked to Br. Nelson), otherwise these are probably fine
    incar:
      prec: 'a'
      #this is the energy cutoff for the planewave basis set.. the default is probably fine but if you want to
      #test this out, see the ref guide to learn some more about this.
      #  encut: 400
      #  isym: 0
      lwave: False
      lreal: 'auto'

      #ediff: 0.00001
      ismear: 1
      sigma: 0.1
    #these are the POTCARS you're gonna use. ask Br. Nelson for the directory to use
    potcars:
      directory: '/apps/restricted/easybuild/software/VASP/5.3.2-ictcet-4.5.0/pot'
      xc: 'PBE'
      #you'll have to open up the POSCARS in the directory and see what the date is at the top
      #of them, and type them here
      versions:
        Au: '04Oct2007'
        Pt: '12Dec2005'
      #there are some ideal setups for different systems, see
      #https://cms.mpi.univie.ac.at/vasp/vasp/Recommended_PAW_potentials_DFT_calculations_using_vasp_5_2.html
      #for the recommended ones. 
      setups:
        Au: ''
        Pt: '_pv'
    kpoints:
      method : 'mueller'
      #there are some methods to determine the best mindistance. See the ref guide to learn more about this..
      #but 70 is probably fine
      mindistance: 70  # Bigger numbers mean denser meshes
      KPPRA: 2000

  #these are the settings for quantum espresso, if you use it. If "qe" isn't in the active section, don't
  #worry about changing this section, it won't read it anyways
  qe:
    pseudopotentials:
      directory: '/home/nelslanc/codes/q-e/pslibrary/pbe/PSEUDOPOTENTIAL'
      versions:
        Au: Au.pbe-spfn-rrkjus_psl.1.0.0.UPF
        Pt: Pt.pbe-spfn-rrkjus_psl.1.0.0.UPF

    kpoints:
      method: 'mp'
      KPPRA: 2000
  #these are the settings for lammps, if you use it. If "lammps" isn't in the active section, don't
  #worry about changing this section, it won't read it anyways
  lammps:
    template: 'lammps.in'
    potential: 'PtAu.eam.alloy'

# Parameters for the job arrays that will be submitted for each
# database. These can be overridden in each database below as well.
  execution:
    template: 'run_array_falcon.sh'
    time: 10 #walltime for calcs. Probably doesn't hurt to make it a little longer than you expect it to take
    ntasks: 1
    nodes: 1 #how many nodes you want to parallelize on. Doesn't help if the code isn't written in parallel.
    mem_per_cpu: 8 #how much memory you'll need for calcs. Better to be safe than sorry on these
    job_name: 'Hf-Ni-Si DB' #Change this for your system. It's what the job will be called 
  #  partition: 'physics'
    array_limit: 150 #if you want to let only a certain amount of calcs in a job array to run at once. 
    #this is the command that will be executed. 
    exec_path: 'vasp6.x' #you may want to add a "> vasp_output" so the output
    #gets written to a file called vasp_output
  #  options:
  #    - "--qos=msg"
  #    - "-C knl"
# Next, we include a list of all the databases we want to create. A
# database following this pattern is created *for each* of the seed
# configurations listed above.
trainingset: #this is the initial enumeration settings
  #The PhononBase class generates the dynamical matrix that is needed
  #by PhononDatabase.
  name: 'enumerated'  # I get to choose the name
  #put the lattice types you want to enumerate here. fcc hcp and bcc are probably fine,
  #but you can add a custom one like is done here, as well.
  lattice:
    - "fcc"
    - "hcp"
    - "bcc"
    - [[0.5,0.5,0],[0.5,0,0.5],[0,0.5,0.5]]
  #fcc hcp and bcc are already known by aBuild. You'll have to include any custom basis though
  basis:
    - None
    - None
    - None
    - [[0,0,0],[0.25,0.25,0.25],[0.75,0.75,0.75]]
  #this is the coordinate system you want to write the POSCARS in. "D" means direct.
  #You could also do "C" for cartesian
  coordsys:
    - "D"
    - "D"
    - "D"
    - "D"
  #custom lattice types need a name. the rest can be given "none"
  name:
    - None
    - None
    - None
    - "fluorite"
#  concs: [ [], [[0,1,2] , [0,1,4]] ] #you can restrict the concentrations here. [0,1,2] means you want to restrict the conc to 0/2-1/2
  nconfigs: [2,2,2,2]  # One number per lattice defined in the lattice variable. These should probably be 0 (to start from empty)
#  siteRestrictions: [['0/1'],['0/1','0/1']] #you can also restrict the sites, not sure how that works though. Ask Br. Nelson
  sizes: [[1,12],[1,6],[1,12],[1,8]] #These are the sizes of cells that will be enumerated
#        ran_seed: 10
gss: # Structures to put in the set of structures for mtp to relax
  name: 'gss'
  #same settings as in trainingset
  lattice:
    - "fcc"
    - "bcc"
    - "hcp"
    - "protos" #protos are unique structures that are kept in a database. Talk to Br. Nelson about whether or not to include these
    - [[0.5,0.5,0],[0.5,0,0.5],[0,0.5,0.5]]
  basis:
    - None
    - None
    - None
    - None
    - [[0,0,0],[0.25,0.25,0.25],[0.75,0.75,0.75]]
  coordsys:
    - "D"
    - "D"
    - "D"
    - "C"
    - "D"
  name:
    - None
    - None
    - None
    - None
    - "fluorite"
#  concs: [ [], [[0,1,2] , [0,1,4]] ]
#  siteRestrictions: [['0/1'],['0/1','0/1']]
  sizes: [[1,12],[1,6],[1,12],[1,10],all]
  nconfigs: [6,6,6,all,6] #these should probably be really large numbers (e.g. 10000)
#this is the set of structures that aren't in the relaxation set but that you want to know the energy of at the end. it's 
holdout:
  name: 'holdout'
  lattice:
    - "sc"
    - "fcc"
    - "bcc"
    - "hcp"
    - "protos"
#  concs: [ [], [[0,1,2] , [0,1,4]] ]
#  siteRestrictions: [['0/1'],['0/1','0/1']]
  sizes: [[1,12],[1,6],[1,12]]
  nconfigs: [100000,100000,100000,100000,all]
fitting:
  pot: 20g.mtp
  dbs: ['*'] 
  execution:
    template: 'run_mtp_ml.sh'
    time: 10 #wall time
    ntasks: 1
    nodes: 1 #a lot of these calcs run faster in parallel. in the ref Guide it will tell you how many nodes is good
    mem_per_cpu: 50 #probably shouldn't need more than about 16 gb, but don't blame me if it uses more
    job_name: 'Ni-Sb-Ti fitting' #change this to something good. 
#  options:
#    - "--qos=msg"
#    - "-C knl"
    modules: ['mpi/openmpi-1.8.5_intel-15.0.2','compiler_intel/2017']
#   
  fits:
    - name: "AgPt" #change this to something good
      dbs: ["*"]
      steps:
        - type: "mtp.MTP"
          selection-limit: 200
          split: "A"
          species:
            - "Ag" #change these to0
            - "Pt"