Input file#

The required settings are provided by input YAML file. This file consists of several sections devoted to setting up particular settings of pacemaker. The sections are listed below.

Cutoff and (optional) metadata#

Global cutoff for the neighborlist constructor is setup as:

cutoff: 10.0

Metadata (optional)

This is arbitrary key (string)-value (string) pairs that would be added to the potential YAML file:

metadata:
  info: some info
  comment: some comment
  purpose: some purpose

Moreover, starttime and user fields would be added automatically

Dataset specification section#

This section is denoted by the key

data:
  ...

Dataset could be saved into file as a pickled pandas dataframe with special names for columns.

data:
  filename: some_stored_dataset.pckl.gzip # or  [dataset1.pckl.gzip, aug_df.pkl.gz]  - multiple datasets are possible to provide
  # aug_factor: 1e-4 # common prefactor for weights of augmented structures (determined by prefix `augmented` in `name` column)
  # ignore_weights: False          # whether to ignore energy and force weighting columns in dataframe
  # datapath: ../data              # path to folder with cache files with pickled dataframes

data:datapath option, if not provided, could be replaced with environment variable $PACEMAKERDATAPATH

Example of creating the subselection of fitting dataframe and saving it is given in examples/data_selection/data_selection.ipynb

Example of generating custom energy/forces weights is given in examples/custom-weights/data_custom_weights.ipynb

Test set#

You could provide test set either as a fraction or certain number of samples from the train set (option test_size) or as a separate pckl.gzip file (option test_filename)

data:
  test_filename: my_test_dataset.pckl.gzip

or

data:
  test_size: 100 # would take 100 samples randomly from train/fit set
  # test_size: 0.1 #  if <1 - would take given fraction of samples randomly from train/fit set

Reference energy#

If provided dataset(s) does not contain corrected energy column, then it can be generated by pacemaker, if you provide reference_energy option, i.e.

data:
  # provide single atom energy and total shift (zero if not specified) 
  reference_energy: { Al: -0.1234, Li: -0.321, shift: 0.134 }

or

data:
  # use constant reference energy for all elements
  reference_energy: 0

or

data:
  # for default values of some common DFT settings
  reference_energy: VASP_PBE_500_0.125_0.1_NM

or

data:
  # for automatic least-square determination of reference energies
  reference_energy: auto

Reference energies (computed or provided) will be added to metadata of potential (in YAML file) and will be automatically extracted from there next time, if no reference_energy option is provided in input.yaml
You can find the resulted reference energies dict in log.txt and provide it manually as a reference_energy option in upfits with updated/extended/new datasets, in order to preserve energy consistency.
If corrected energy-per-atom values are lower than -20 eV/atom and higher than +250 eV/atom, then warning will be shown and reference_energy: auto option will be used.

Interatomic potential (or B-basis) configuration#

Basis configuration#

In order to specify the B-basis potential, you have to provide four main components (aka basis shape ): elements, embeddings for each element, bonds for each possible pairs of elements and functions for each possible combination of elements (unary, binary, ternary, etc.) as follows:

potential:
  deltaSplineBins: 0.001
  elements: [ Al, Ni ]  # list of all element

  # Embeddings are specified for each individual elements,
  # all parameters could be distinct for different species
  embeddings: ## possible keywords: ALL, UNARY, elements: Al, Ni
    Al: {
      npot: 'FinnisSinclairShiftedScaled',
      fs_parameters: [ 1, 1, 1, 0.5 ], ## non-linear embedding function: 1*rho_1^1 + 1*rho_2^0.5
      ndensity: 2,

      # core repulsion parameters
      rho_core_cut: 200000,
      drho_core_cut: 250
    }

    Ni: {
      npot: 'FinnisSinclairShiftedScaled', ## linear embedding function: 1*rho_1^1
      fs_parameters: [ 1, 1 ],
      ndensity: 1,

      # core repulsion parameters
      rho_core_cut: 3000,
      drho_core_cut: 150
    }

  ## Bonds are specified for each possible pairs of elements
  ## One could use keywords: ALL (Al,Ni, AlNi, NiAl)
  bonds: ## possible keywords: ALL, UNARY, BINARY, elements pairs as AlAl, AlNi, NiAl, etc...  
    ALL: {
      radbase: ChebExpCos,
      radparameters: [ 5.25 ],

      ## outer cutoff
      rcut: 5,
      dcut: 0.01,

      ## inner cutoff  [r_in - delta_in, r_in] - transition region from ACE to core-repulsion
      # at r < r_in-delta_in - no ACE interaction, only core-repulsion
      r_in: 1.0,
      delta_in: 0.5,


      ## core-repulsion parameters `prefactor` and `lambda` in
      ## prefactor*exp(-lambda*r^2)/r, > 0 only if r < r_in - delta_in
      core-repulsion: [ 100.0, 5.0 ],
    }

    ## BINARY overwrites ALL settings when they are repeated
    BINARY: {
      radbase: ChebPow,
      radparameters: [ 6.25 ],

      ## cutoff may vary for different bonds
      rcut: 5.5,
      dcut: 0.01,

      ## inner cutoff, applied in a range [r_in - delta_in, r_in]
      r_in: 1.0,
      delta_in: 0.5,

      ## core-repulsion parameters `prefactor` and `lambda` in
      ## prefactor*exp(-lambda*r^2)/r,> 0 only if r < r_in - delta_in
      core-repulsion: [ 10.0, 5.0 ],
    }

  ## possible keywords: ALL, UNARY, BINARY, TERNARY, QUATERNARY, QUINARY,
  ##  element combinations as (Al,Al), (Al, Ni), (Al, Ni, Zn), etc...
  functions:
    # number_of_functions_per_element: 700  # specify the total number of functions per element to keep
    UNARY: {
      nradmax_by_orders: [ 15, 3, 2, 2, 1 ],
      lmax_by_orders: [ 0, 2, 2, 1, 1 ],
      # coefs_init: zero # initialization of functions coefficients: zero (default) or random
    }

    BINARY: {
      nradmax_by_orders: [ 15, 2, 2, 2 ],
      lmax_by_orders: [ 0, 2, 2, 1 ],
      # coefs_init: zero # initialization of functions coefficients: zero (default) or random
    }

In sections embeddings, bonds and functions one could use keywords (ALL, UNARY, BINARY, TERNARY, QUATERNARY, QUINARY). The settings provided by more specific keyword will override those from less specific keyword, i.e. ALL < UNARY < BINARY < ('Al','Ni')

Upfitting#

If you want to continue the fitting of the existing potential from potential.yaml file, then specify

potential: potential yaml

alternatively, one could use pacemaker ... -p potential.yaml option.

For specifying both initial and target potential from the file one could provide:

potential:
  filename: potential.yaml

  ## in "ladder" fitting scheme, potential from with to start fit
  # initial_potential: initial_potential.yaml

  ## reset potential from potential.yaml, i.e. set radial coefficients to delta_nk and func coeffs=[0..]
  # reset: true

or alternatively, one could use pacemaker ... -p potential.yaml -ip initial_potential.yaml options.

Fitting settings#

Example of fit section is:

fit:
  ## LOSS FUNCTION OPTIONS ##
  loss: {
    ## [0..1] or auto, relative force weight,
    ## kappa = 0 - energies-only fit,
    ## kappa = 1 - forces-only fit
    ## auto - determined from dataset based on variance of energies and forces
    kappa: 0,
    ## L1-regularization coefficient
    L1_coeffs: 0,
    ## L2-regularization coefficient
    L2_coeffs: 0,
    ## w0 radial smoothness regularization coefficient
    w0_rad: 0,
    ## w1 radial smoothness regularization coefficient
    w1_rad: 0,
    ## w2 radial smoothness regularization coefficient
    w2_rad: 0
  }

  ## DATA WEIGHTING OPTIONS ##
  weighting: {
    ## weights for the structures energies/forces are associated according to the distance to E_min:
    ## convex hull ( energy: convex_hull) or minimal energy per atom (energy: cohesive)
    type: EnergyBasedWeightingPolicy,
    ## number of structures to randomly select from the initial dataset
    nfit: 10000,
    ## only the structures with energy up to E_min + DEup will be selected
    DEup: 10.0,  ## eV, upper energy range (E_min + DElow, E_min + DEup)        
    ## only the structures with maximal force on atom  up to DFup will be selected
    DFup: 50.0, ## eV/A
    ## lower energy range (E_min, E_min + DElow)
    DElow: 1.0,  ## eV
    ## delta_E  shift for weights, see paper
    DE: 1.0,
    ## delta_F  shift for weights, see paper
    DF: 1.0,
    ## 0<wlow<1 or None: if provided, the renormalization weights of the structures on lower energy range (see DElow)
    wlow: 0.75,
    ##  "convex_hull" or "cohesive" : method to compute the E_min
    energy: convex_hull,
    ## structures types: all (default), bulk or cluster
    reftype: all,
    ## random number seed
    seed: 42
  }

  ## Custom weights:  corresponding to main dataset index and `w_energy` and `w_forces` columns should
  ## be provided in pckl.gzip file
  #weighting: {type: ExternalWeightingPolicy, filename: custom_weights_only.pckl.gzip}

  ## OPTIMIZATION OPTIONS ##
  optimizer: BFGS # BFGS, L-BFGS-B, Nelder-Mead, etc. : scipy minimization algorithm
  ## additional options for scipy.minimize(..., options={...}, ...)
  #options: {maxcor: 100}    
  maxiter: 1000 # maximum number of iteration for EACH scipy minimization round

  ## EXTRA OPTIONS ##
  repulsion: auto            # set inner cutoff based on the minimal distance in the dataset

    #trainable_parameters: ALL  # ALL, UNARY, BINARY, ..., radial, func, {"AlNi": "func"}, {"AlNi": {"func","radial"}}, ...

    ##(optional) number of consequentive runs of fitting algorithm (for each ladder step), that helps convergence
    #fit_cycles: 1   

    ## starting from second fit_cycle:

    ## applies Gaussian noise with specified relative sigma/mean ratio to all potential trainable coefficients
    #noise_relative_sigma: 1e-3

    ## applies Gaussian noise with specified absolute sigma to all potential trainable coefficients
    #noise_absolute_sigma: 1e-3  

    # reset the function coefficients according to Gaussian distribution with given sigma; enable ensemble fitting mode
    #randomize_func_coeffs: 1e-3  

    ## LADDER SCHEME (i.e. hierarchical fitting) ##      
    ## enables hierarchical fitting (LADDER SCHEME), that sequentially add specified number of B-functions (LADDER STEP)    
    #ladder_step: [10, 0.02]  
    ##      - integer >= 1 - number of basis functions to add in ladder scheme,
    ##      - float between 0 and 1 - relative ladder step size wrt. current basis step
    ##      - list of both above values - select maximum between two possibilities on each iteration 
    ##     see. Ladder scheme fitting for more info


    ## Possible values:
    ## body_order  -  new basis functions are added according to the body-order, i.e., a function with higher body-order
    ##                will not be added until the list of functions of the previous body-order is exhausted
    ## power_order -  the order of adding new basis functions is defined by the "power rank" p of a function.
    ##                p = len(ns) + sum(ns) + sum(ls). Functions with the smallest p are added first      
  #ladder_type: body_order    


  ## callbacks during the fitting. Module quick_validation.py should be available for import
  ## see example/pacemaker_with_callback for more details and examples
  #callbacks:
  #  - quick_validation.test_fcc_potential_callback

If not specified, then uniform weight and energy-only fit (kappa=0), fit_cycles=1, noise_relative_sigma = 0 settings will be used.

If ladder fitting scheme is used, then intermediate version of the potential after each ladder step will be saved into interim_potential_ladder_step_{LADDER_STEP}.yaml.

Backend specification#

backend:
  evaluator: tensorpot

  ## for `tensorpot` evaluator, following options are available:
  # batch_size: 10            # batch size for loss function evaluation, default is 10
  # batch_size_reduction: True # automatic batch_size reduction if not enough memory (default - True) 
  # batch_size_reduction_factor: 1.618  # batch size reduction factor
  # display_step: 20          # frequency of detailed metric calculation and printing

Alternatively, backend could be selected as pacemaker ... -b tensorpot

Ladder (hiererchical) basis extension#

In a ladder scheme potential extension happens by adding new portion of basis functions step-by-step, to form a "ladder" from initial potential to final potential. Following settings should be added to the input YAML file:

Specify final potential shape by providing potential section:

potential:
  deltaSplineBins: 0.001
  element: Al
  ...

Specify initial potential by providing initial_potential option in potential section:

potential:
  ...
  initial_potential: some_start_or_interim_potential.yaml    # potential to start fit from

If initial potential is not specified, then the fit will start from empty potential. Alternatively, you can specify initial potential by command-line option

pacemaker ... -ip some_start_or_interim_potential.yaml

Specify ladder_step in fit section:

fit:
  ...

  ladder_step: [ 10, 0.02 ]
## Possible values:
##  - integer >= 1 - number of basis functions to add in ladder scheme,
##  - float between 0 and 1 - relative ladder step size wrt. current basis step
##  - list of both above values - select maximum between two possibilities on each iteration