nvt

Thermostats

Classes

AndersenThermostat	Specialized Verlet hook.
BerendsenThermostat	Specialized Verlet hook.
LangevinThermostat	Specialized Verlet hook.
CSVRThermostat	Specialized Verlet hook.
GLEThermostat	Specialized Verlet hook.
NHChain	Base class for dataclasses that should act like a JAX pytree node.
NHCThermostat	Specialized Verlet hook.
NHCAttributeStateItem	Base class for dataclasses that should act like a JAX pytree node.

Module Contents

class nvt.AndersenThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

select: jax.Array | None = None

annealing: jax.Array

This is an implementation of the Andersen thermostat. The method is described in:

Andersen, H. C. J. Chem. Phys. 1980, 72, 2384-2393.

Arguments:

temp

The average temperature of the NVT ensemble

Optional arguments:

start

The first iteration at which this hook is called

step

The number of iterations between two subsequent calls to this hook.

select

An array of atom indexes to indicate which atoms controlled by the thermostat.

annealing

After every call to this hook, the temperature is multiplied with this annealing factor. This effectively cools down the system.

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

class nvt.BerendsenThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

timecon: jax.Array

This is an implementation of the Berendsen thermostat. The algorithm is described in:

Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690

Arguments:

temp

The temperature of thermostat.

Optional arguments:

start

The step at which the thermostat becomes active.

timecon

The time constant of the Berendsen thermostat.

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

class nvt.LangevinThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

key: jax.Array

timecon: jax.Array

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

thermo(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

class nvt.CSVRThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

timecon: jax.Array

kin: jax.Array | None = None

key: jax.Array

This is an implementation of the CSVR thermostat. The equations are

derived in:

Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126, 014101

The implementation (used here) is derived in

Bussi, G.; Parrinello, M. Comput. Phys. Commun. 2008, 179, 26-29

Arguments:

temp

The temperature of thermostat.

Optional arguments:

start

The step at which the thermostat becomes active.

timecon

The time constant of the CSVR thermostat.

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

class nvt.GLEThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

timecon: jax.Array

kin: jax.Array | None = None

a_p: jax.Array

c_p: jax.Array | None = None

ns: int | None = None

key: jax.Array

t: jax.Array | None = None

S: jax.Array | None = None

n_atoms: int | None = None

This hook implements the coloured noise thermostat. The equations are derived in:

Ceriotti, M.; Bussi, G.; Parrinello, M J. Chem. Theory Comput. 2010, 6, 1170-1180.

Arguments:

temp

The temperature of thermostat.

a_p

Square drift matrix, with elements fitted to the specific problem.

Optional arguments:

c_p

Square static covariance matrix. In equilibrium, its elements are fixed. For non-equilibrium dynamics, its elements should be fitted.

start

The step at which the thermostat becomes active.

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

thermo(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

class nvt.NHChain(*args, **kwargs)

Bases: IMLCV.base.datastructures.MyPyTreeNode

Base class for dataclasses that should act like a JAX pytree node.

length: int = 3

timestep: jax.Array

temp: jax.Array

timecon: jax.Array

restart_pos: bool = False

restart_vel: bool = False

pos0: jax.Array | None = None

vel0: jax.Array | None = None

pos: jax.Array | None = None

vel: jax.Array | None = None

masses: jax.Array | None = None

ndof: int = 0

key: jax.Array

__post_init__()

set_ndof(ndof: int) → NHChain

get_random_vel_therm() → tuple[jax.Array, NHChain]

update(ekin, vel, G1_add) → tuple[jax.Array, jax.Array, NHChain]

get_econs_correction()

class nvt.NHCThermostat(*args, **kwargs)

Bases: IMLCV.new_yaff.verlet.ThermostatHook

Specialized Verlet hook.

This is mainly used for the implementation of thermostats and barostats.

name: str

kind: str

method: str

chain: NHChain

This hook implements the Nose-Hoover chain thermostat. The equations are derived in:

Martyna, G. J.; Klein, M. L.; Tuckerman, M. J. Chem. Phys. 1992, 97, 2635-2643.

The implementation (used here) of a symplectic integrator of the Nose-Hoover chain thermostat is discussed in:

Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 87, 1117-1157.

Arguments:

temp

The temperature of thermostat.

Optional arguments:

start

The step at which the thermostat becomes active.

timecon

The time constant of the Nose-Hoover thermostat.

chainlength

The number of beads in the Nose-Hoover chain.

chain_pos0

The initial thermostat chain positions

chain_vel0

The initial thermostat chain velocities

restart

Indicates whether the initalisation should be carried out

init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None)

class nvt.NHCAttributeStateItem(*args, **kwargs)

Bases: IMLCV.new_yaff.iterative.StateItem

Base class for dataclasses that should act like a JAX pytree node.

attr: str

get_value(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)