Updater

Overview

plugin_muMC.update.StateDescriptor

Describes bead states available to a ManyStateSwitcher.

plugin_muMC.update.BilayerInverter

Flips lipids between leaflets

Details

class plugin_muMC.update.BilayerInverter(molecules, leaflet)

Bases: plugin_muMC.update._updater

Flips lipids between leaflets

After flip() is called, this updater will select between 1 and maxFlips lipids from a leaflet and brutally flip them to the opposite leaflet within the next 100 timesteps.

Parameters
flip()

Perform a flip event within the next 100 timesteps

Returns

setMaxFlips(max_value)

Set the maximum number of flips per update

Parameters

max_value (int) – largest number (default = 1)

Returns

class plugin_muMC.update.ManyStatesSwitcher(group, molecules, descriptor, seed=numpy.random.randint, stateNames=None, period=20, phase=0, kT=1.0, name=None)

Bases: plugin_muMC.update._updater

Attempts swaps between molecules chemical states to enforce a semi-grand canonical ensemble

The semi-grand canonial ensemble can be used to change bead nature (non-bonded interactions) as well as angle potentials. In the latter case, it will swap angles where the bead is centered on. If we consider a set of molecules comprised of three beads of type A and B and angles ‘A’ and ‘B’, potential molecules types are AAA (with angle ‘A’), AAB (with angle ‘A’) ABA (with angle ‘B’), ABB (with angle ‘B’), … Note that in this case AAB and BAA would be different molecules.

The semi-grand canonical ensemble can swap angle and/or bead types independently, i.e., one of the sets of lists may be left empty.

Different ensembles can be used for different parts of the molecule. In such cases, they should be executed on different phases

Parameters

  • group (hoomd.group.group) – group on which to perform MC swaps

  • molecules (collectives.Molecules) – molecule descriptors

  • descriptor (StateDescriptor) – description of the available states

  • seed (int) – seed for RNG generation

  • stateNames (list[str]) – List of names associated with the different states. This is used to generate fragment description, in turn used to translate hash values into chemical information. Defaults to combination of angle and chemical types

  • period (int) – MC update frequency

  • phase (int) – When -1, start on the current time step. When >= 0, execute on steps where (step + phase) % period == 0. (see standard hoomd updater configuration)

  • kT (float) – temperature of the updater, used to compute probability exp(-E / kT)

  • name (str) – Suffix of name of this set of chemical potentials for fragment based chemical potential setting (see Molecules objects). Name of the fragment is SGC+name

setRCut(value)

Set minimal cell width for checkerboard decomposition. This value should be at least equal to interaction length

Parameters

value (float) – Rcut value

Returns

set_params(kT=None)

Sets semi-grand canonical parameter kT :param kT: Simulation temperature :return:

update_molecules()

Recompute states, for instance after restoring a snapshot

Returns

class plugin_muMC.update.StateDescriptor(charges=None, charge_force=None, types=None, type_force=None, angles=None, angle_force=None)

Bases: object

Describes bead states available to a ManyStateSwitcher.

The description is a series of lists (or None) of equal length. Index 0 of every list will describe state 0 and so on. The MC update force objects need to be passed as lists as well, with the notable exception of charge, which is a single entity since the force only depends on charge.

Parameters

  • charges (list[float]) – List of charges, in simulation units (e.g. [0, 0.23, -0.23])

  • charge_force (pair.charge_mc) – MC computation of charge changes

  • types (list[str]) – List of beadtypes

  • type_force (list[pair.lj_mc]) – force objects associated with type change for MC updates

  • angles (list[str]) – List of angle types (eg [‘Sat180’, ‘Unsat120’])

  • angle_force (list[angle.cosinesq]) – force objects associated with angle changes for MC updates