high_throughput_predict

class HtAds(object)

High-throughput predictions.

__init__(self, **hp_config)

See https://jzhang-github.github.io/AGAT/Default%20parameters.html#default-high-throughput-config for more details.

geo_opt(atoms_with_calculator, **kwargs)

Geometrical optimization of given structure.

Note

BFGS optimizer is adopted.

Parameters:

• atoms_with_calculator (ase.atoms) – structure with ase.calculators attribute.

• **kwargs (dict/args) –

  relaxation configuration.

  Hint

  You can find detailed settings of BFGS. Here is the summary:

  Setting	Default	Description
  fmax	0.05	Maximum force acting on every atom should be lower than this.
  steps	200	Stop optimization if iteration step is reached.
  maxstep	0.1	Used to set the maximum distance an atom can move per iteration
  restart	None	Pickle file used to store hessian matrix. If set, file with such a name will be searched and hessian matrix stored will be used, if the file exists.
  restart_steps	5	In some cases, it can be difficult for BFGS to converge. If BFGS cannot coverge after steps, this code halves maxstep and rerun. But this code will not rerun more than restart_steps times.
  perturb_steps	0	Defines how many perturbated structures (perturb free atoms only) are optimized. Only structure with lowest energy is adopted.
  perturb_amplitude	0.05	perturbation amplitude

Returns:

• energy: energy after relaxation

• force: atomic forces after relaxation.

• force_max: max atomic force after relaxation.

ads_calc(formula, calculator, **kwargs)

BFGS calculations including geometrical optimizations of bulk, clean surface, and adsorption strucures.

Parameters:

• formula (str) – chemical formula.

• calculator (ase.calculators) – calculator.

• **kwargs (dict/args) –

  relaxation configuration.

  Hint

  Details of relaxation configuration:

  Setting	Default	Description
  calculation_index	None	Calculation index. You can use this parameter to differentiate multiple calculations.
  fix_surface_atom	False	Fix all surface atoms if this is True.
  remove_bottom_atoms	False	Remove the bottom atomic plane if this is True.
  save_trajectory	False	Save relaxation trajectory or not.
  partial_fix_adsorbate	False	Partially fix adsorbate positions.
  adsorbates	[‘O’, ‘OH’, ‘OOH’]	Adsorbates placed on the surface.
  sites	[‘ontop’, ‘bridge’, ‘hollow’]	Sites for placing adsorbates.
  fmax	0.1	Maximum force acting on every atom should be lower than this.
  dist_from_surf	2.0	Distance between adsorbate and surface.

run(self, formula, **kwargs)

Parameters:

formula (str) – Input chemical formula