npt

npt#

Barostats

Classes#

`TBCombination`	Specialized Verlet hook.
`McDonaldBarostat`	Specialized Verlet hook.
`BerendsenBarostat`	Specialized Verlet hook.
`LangevinBarostat`	Specialized Verlet hook.
`MTKBarostat`	Specialized Verlet hook.
`PRBarostat`	Specialized Verlet hook.
`TadmorBarostat`	Specialized Verlet hook.
`MTKAttributeStateItem`	Base class for dataclasses that should act like a JAX pytree node.

Module Contents#

class npt.TBCombination(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

temp: jax.Array#

press: jax.Array#

thermostat: IMLCV.new_yaff.verlet.ThermostatHook#

barostat: IMLCV.new_yaff.verlet.BarostatHook#

step_thermo: jax.Array#

step_baro: jax.Array#

baro_expects_call: bool#

thermo_expects_call: bool#

chainvel0: jax.Array | None = None#

G1_add: jax.Array | None = None#

VerletHook combining an arbitrary Thermostat and Barostat instance, which ensures these instances are called in the correct succession, and possible coupling between both is handled correctly.

Arguments:

thermostat: A Thermostat instance
barostat: A Barostat instance

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

__call__(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)#

verify()#

class npt.McDonaldBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

kind: str#

method: str#

amp: jax.Array#

dim: int | None = 3#

key: jax.Array#

this code is not fully tested yet!

Arguments:

temp: The average temperature of the jnp. ensemble
press: The external pressure of the jnp. 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.
amp: The amplitude of the changes in the logarithm of the volume.

Type:: Warning

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

class npt.BerendsenBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

kind: str#

method: str#

timecon_press: jax.Array#

beta: jax.Array#

anisotropic: bool#

vol_constraint: bool#

mass_press: jax.Array | None = None#

cell: jax.Array | None = None#

This hook implements the Berendsen barostat. The equations are derived 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:

ff: A ForceField instance.
temp: The temperature of thermostat.
press: The applied pressure for the barostat.

Optional arguments:

start: The step at which the thermostat becomes active.
timecon: The time constant of the Berendsen barostat.
beta: The isothermal compressibility, conventionally the compressibility of liquid water
anisotropic: Defines whether anisotropic cell fluctuations are allowed.
vol_constraint: Defines whether the volume is allowed to fluctuate.

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

class npt.LangevinBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

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#

anisotropic: bool#

vol_constraint: bool#

vel_press: jax.Array#

timestep_press: jax.Array | None = None#

mass_press: jax.Array#

This hook implements the Langevin barostat. The equations are derived in:

Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621

Arguments:

ff: A ForceField instance.
temp: The temperature of thermostat.
press: The applied pressure for the barostat.

Optional arguments:

start: The step at which the barostat becomes active.
timecon: The time constant of the Langevin barostat.
anisotropic: Defines whether anisotropic cell fluctuations are allowed.
vol_constraint: Defines whether the volume is allowed to fluctuate.

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0)#

getR()#

class npt.MTKBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

kind: str#

method: str#

key: jax.Array#

cell: jax.Array | None = None#

timecon: jax.Array#

anisotropic: bool#

vol_constraint: bool#

vel_press: jax.Array#

baro_thermo: IMLCV.new_yaff.nvt.NHCThermostat | None = None#

timecon_press: jax.Array#

This hook implements the Martyna-Tobias-Klein barostat. The equations are derived in:

Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189.

The implementation (used here) of a symplectic integrator of this barostat is discussed in

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

Arguments:

ff: A ForceField instance.
temp: The temperature of thermostat.
press: The applied pressure for the barostat.

Optional arguments:

start: The step at which the barostat becomes active.
timecon: The time constant of the Martyna-Tobias-Klein barostat.
anisotropic: Defines whether anisotropic cell fluctuations are allowed.
vol_constraint: Defines whether the volume is allowed to fluctuate.
baro_thermo: NHCThermostat instance, coupled directly to the barostat
vel_press0: The initial barostat velocity tensor
restart: If true, the cell is not symmetrized initially

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0)#

add_press_cont()#

_compute_ekin_baro()#

class npt.PRBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

kind: str#

method: str#

timecon_press: jax.Array#

anisotropic: bool#

vol_constraint: bool#

mass_press: jax.Array | None = None#

cell: jax.Array | None = None#

baro_thermo: IMLCV.new_yaff.nvt.NHCThermostat | None = None#

P: jax.Array | None = None#

S_ani: jax.Array | None = None#

cellinv0: jax.Array | None = None#

vol0: jax.Array | None = None#

Sigma: jax.Array | None = None#

vel_press: jax.Array | None = None#

This hook implements the Parrinello-Rahman barostat for finite strains. The equations are derived in:

Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190.

Arguments:

ff: A ForceField instance.
temp: The temperature of thermostat.
press: The applied pressure for the barostat.

Optional arguments:

start: The step at which the barostat becomes active.
timecon: The time constant of the Tadmor-Miller barostat.
anisotropic: Defines whether anisotropic cell fluctuations are allowed.
vol_constraint: Defines whether the volume is allowed to fluctuate.
baro_thermo: NHCThermostat instance, coupled directly to the barostat
vel_press0: The initial barostat velocity tensor
restart: If true, the cell is not symmetrized initially

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0)#

add_press_cont()#

_compute_ekin_baro()#

class npt.TadmorBarostat(*args, **kwargs)#

Bases: IMLCV.new_yaff.verlet.BarostatHook

Specialized Verlet hook.

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

name: str#

kind: str#

method: str#

timecon_press: jax.Array | float = 41341.37333664682#

anisotropic: bool#

vol_constraint = False#

mass_press: jax.Array | float | None = None#

baro_thermo: IMLCV.new_yaff.nvt.NHCThermostat | None = None#

vel_press: jax.Array | None = None#

cell: jax.Array | None = None#

cellinv0: jax.Array | None = None#

Strans: jax.Array | None = None#

Vol0: jax.Array | None = None#

key: jax.Array#

This hook implements the Tadmor-Miller barostat for finite strains. The equations are derived in:

Tadmor, E. B.; Miller, R. E. Modeling Materials: Continuum, Atomistic and Multiscale Techniques 2011, 520-527.

Arguments:

ff: A ForceField instance.
temp: The temperature of thermostat.
press: The applied second Piola-Kirchhoff tensor for the barostat.

Optional arguments:

start: The step at which the barostat becomes active.
timecon: The time constant of the Tadmor-Miller barostat.
anisotropic: Defines whether anisotropic cell fluctuations are allowed.
vol_constraint: Defines whether the volume is allowed to fluctuate.
baro_thermo: NHCThermostat instance, coupled directly to the barostat
vel_press0: The initial barostat velocity tensor
restart: If true, the cell is not symmetrized initially

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

pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None)#

baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0)#

add_press_cont()#

_compute_ekin_baro()#

_compute_angular_tensor(pos, vel, masses)#

class npt.MTKAttributeStateItem(*args, **kwargs)#

Bases: IMLCV.new_yaff.iterative.StateItem

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

key: str = 'MTKattr'#

attr: str#

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