Widom Class

The Widom class serves as the main interface for handling Widom insertion simulation logic.

class flames.widom.Widom(framework_atoms, adsorbate_atoms, temperature, model, vdw_radii, framework_energy=None, adsorbate_energy=None, vdw_factor=0.6, max_overlap_tries=1000, max_deltaE=1.555, device='cpu', save_snapshots=True, save_rejected=False, output_to_file=True, output_folder=None, debug=False, random_seed=None, cutoff_radius=6.0, automatic_supercell=True)[source]

Bases: BaseSimulator

Base class for Widom insertion method using ASE.

This class performs the Widom insertion method to calculate the enthalpy of adsorption and Henry coefficient of an adsorbate in a framework.

Currently, it supports only one adsorbate molecule and any ASE-compatible calculator for energy calculations.

Parameters:

  • framework_atoms (ase.Atoms) – The empty framework structure where the adsorbate will be inserted.

  • adsorbate_atoms (ase.Atoms) – The adsorbate molecule to be inserted into the framework.

  • temperature (float) – Temperature of the ideal reservoir in Kelvin.

  • model (ase.calculators.calculator.Calculator) – ASE-compatible calculator for energy calculations.

  • vdw_radii (np.ndarray) – Van der Waals radii of the atoms in the framework and adsorbate.

  • framework_energy (float or None, optional) – Pre-calculated potential energy of the empty framework in eV. If not provided, it will be calculated during initialization.

  • adsorbate_energy (float or None, optional) – Pre-calculated potential energy of the adsorbate molecule in eV. If not provided, it will be calculated during initialization.

  • vdw_factor (float, optional) – Factor to scale the Van der Waals radii. Default is 0.6.

  • max_overlap_tries (int, optional) – Maximum number of tries to insert/move a molecule without overlap. Default is 100.

  • max_deltaE (float, optional) – Maximum energy difference (in eV) to consider for acceptance criteria. This is used to avoid overflow due to problematic calculations. Default is 1.555 eV (approx. 150 kJ/mol).

  • device (str, optional) – Device to run the calculations on, either 'cpu' or 'cuda'. Default is 'cpu'.

  • save_snapshots (bool, optional) – Whether to save the simulation state and results. Default is True.

  • save_rejected (bool, optional) – If True, saves the rejected moves in a trajectory file. Default is False.

  • output_to_file (bool, optional) – If True, writes the output to a file named Widom_Output.out in the results directory. Default is True.

  • output_folder (str or None, optional) – Folder to save the output files. If None, a folder named results_<T>_<P> will be created.

  • debug (bool, optional) – If True, enables debug mode with more verbose output. Default is False.

  • random_seed (int or None, optional) – Random seed for reproducibility. Default is None.

  • cutoff_radius (float, optional) – Interaction potential cut-off radius used to estimate the minimum unit cell. Default is 6.0.

  • automatic_supercell (bool, optional) – Whether to automatically create a supercell based on the cutoff radius. Default is True.

get_framework_mass()

Calculate the mass of the framework in kg.

Returns:

The mass of the framework in kg.

Return type:

float

get_ideal_supercell()

Get the ideal supercell dimensions based on the cutoff radius.

Returns:

An array of three integers representing the number of unit cells in each dimension.

Return type:

np.ndarray

npt(nsteps, time_step=0.5, mode='iso_shape', driver='MTKNPT', set_momenta=True, output_interval=100, movie_interval=100, calculator=None, **kwargs)

Run a NPT simulation using the Berendsen thermostat and barostat.

Parameters:

  • nsteps (int) – Number of steps to run the NPT simulation.

  • time_step (float, optional) – Time step for the NPT simulation (default is 0.5 fs).

  • mode (str, optional) – The mode of the NPT simulation (default is “iso_shape”). Can be one of “iso_shape”, “aniso_shape”, or “aniso_flex”.

  • driver (str, optional) – The driver to use for the NPT simulation. Can be Berendsen, NoseHoover or MTKNPT (default is “MTKNPT”).

  • set_momenta (bool, optional) – Whether to set the atomic momenta to a Maxwell-Boltzmann distribution of the simulation temperature.

  • output_interval (int, optional) – The interval for logging output (default is 100 steps).

  • movie_interval (int, optional) – The interval for saving trajectory frames (default is 100 step).

  • calculator (ase.calculators.calculator.Calculator or None, optional) – The calculator to use for energy calculations. If None, the default model will be used.

  • kwargs (optional) – Arguments passed to the ase molecular dynamics class.

nvt(nsteps, time_step=0.5, set_momenta=True, output_interval=100, movie_interval=100, calculator=None, **kwargs)

Run a NVT simulation using the Berendsen thermostat.

Parameters:

  • nsteps (int) – Number of steps to run the NVT simulation.

  • time_step (float, optional) – Time step for the NVT simulation (default is 0.5 fs).

  • set_momenta (bool, optional) – Whether to set the atomic momenta to a Maxwell-Boltzmann distribution of the simulation temperature.

  • output_interval (int, optional) – The interval for logging output (default is 100 steps).

  • movie_interval (int, optional) – The interval for saving trajectory frames (default is 100 step).

  • calculator (ase.calculators.calculator.Calculator or None, optional) – The calculator to use for energy calculations. If None, the default model will be used.

  • kwargs (optional) – Arguments passed to the ase molecular dynamics class.

optimize_adsorbate(max_steps=1000, max_force=0.05)

Optimize the adsorbate structure using the provided calculator.

Parameters:

  • max_steps (int, optional) – Maximum number of optimization steps (default is 1000).

  • symm_tol (float, optional) – Tolerance for symmetry (default is 1e-3).

  • max_force (float, optional) – Maximum force tolerance for convergence (default is 0.05 eV/Å).

Returns:

The optimized adsorbate structure.

Return type:

ase.Atoms

optimize_framework(max_steps=1000, opt_cell=True, fix_symmetry=True, hydrostatic_strain=True, symm_tol=0.001, max_force=0.05)

Optimize the framework structure using the provided calculator.

Parameters:

  • max_steps (int, optional) – Maximum number of optimization steps (default is 1000).

  • tol (float, optional) – Tolerance for convergence (default is 1e-5).

Returns:

The optimized framework structure.

Return type:

ase.Atoms

restart()[source]

Restart the simulation from the last state.

This method loads the last saved state from the trajectory file and restores the simulation to that state. It also loads the uptake, total energy, and total adsorbates lists from the saved files if they exist.

Return type:

None

run(N)[source]
Return type:

None

save_results(file_name='Widom_Results.json')[source]

Save a json file with the main results of the simulation.

Parameters:

file_name (str, optional) – Name of the output json file (default is ‘Widom_Results.json’).

Return type:

None

set_adsorbate(adsorbate_atoms, adsorbate_energy=None, n_adsorbates=0)

Set the adsorbate structure for the simulation.

Parameters:

  • adsorbate_atoms (ase.Atoms) – The new adsorbate structure as an ASE Atoms object.

  • adsorbate_energy (float or None, optional) – The energy of the adsorbate in eV. If None, the energy will be calculated using the provided model.

  • n_adsorbates (int) – Number of adsorbate molecules in the framework.

Return type:

None

set_framework(framework_atoms, framework_energy=None)

Set the framework structure for the simulation.

Parameters:

  • framework_atoms (ase.Atoms) – The new framework structure as an ASE Atoms object.

  • framework_energy (float or None, optional) – The energy of the framework in eV. If None, the energy will be calculated using the provided model.

Return type:

None

set_state(state)

Set the current state of the simulation.

Parameters:

state (ase.Atoms) – The current state of the simulation as an ASE Atoms object.

Return type:

None

step(iteration)[source]

Run a single iteration of the Widom insertion method.

Parameters:

iteration (int) – The current iteration number.

Return type:

None

try_insertion()[source]

Try to insert a new adsorbate molecule into the framework. This method randomly places the adsorbate in the framework and checks for van der Waals overlap. If there is no overlap, it calculates the new potential energy and decides whether to accept the insertion based on the acceptance criteria.

Return type:

tuple[float, Atoms]

Returns:

  • deltaE (float) – The change in energy associated with the insertion. If the insertion fails, returns a large value (1000.0).

  • atoms_trial (ase.Atoms) – The trial configuration after the insertion attempt.

update_statistics(deltaE)[source]

Update the statistics of the Widom insertion method after a new insertion.

Parameters:

deltaE (float) – The change in energy associated with the latest insertion.

Return type:

None