protex.update.KeepHUpdate

class protex.update.KeepHUpdate(ionic_liquid: ProtexSystem, all_forces: bool = False, to_adapt: list[tuple[str, int, frozenset[str]]] | None = None, include_equivalent_atom: bool = False, reorient: bool = False, K: int = 300)[source]

Bases: Update

KeepHUpdate performs updates but uses the original H position. Keep the position of the original H when switching from dummy to real H.

Parameters:

  • ionic_liquid (ProtexSystem) – An instance of ProtexSystem

  • all_forces (bool = False) – Whether to update all forces or just the nonbonded forces.

  • to_adapt (list[tuple[str, int, frozenset[str]]] | None = None) – The number of the given species will be kept close to the given value by changing the probability of the given reaction. prob_new = prob_orig + K*( x(t) / x(eq) - 1)^3

  • include_equivalent_atom (bool = False) – Whether to consider equivalent atoms for the distance check.

  • reorient (bool = False) – Whether to reorient the molecule if the equivalent atom was used, or just switch the dummy atoms on/off.

  • K (int = 300) – The factor for adapting the probabilities based on the concentration of certain species.

Methods

dump

Pickle a KeepHUpdate instance.

load

Load a pickled KeepHUpdate instance.
dump(fname: str) → None[source]

Pickle a KeepHUpdate instance.

Parameters:

fname (str) – The file name

static load(fname, protex_system: ProtexSystem) → KeepHUpdate[source]

Load a pickled KeepHUpdate instance.

Parameters:

  • fname (str) – The file name

  • protex_system (ProtexSystem) – An instance of ProtexSystem, used to create the Update instance

Returns:

An update instance

Return type:

KeepHUpdate