nvt === .. py:module:: nvt .. autoapi-nested-parse:: Thermostats Classes ------- .. autoapisummary:: nvt.AndersenThermostat nvt.BerendsenThermostat nvt.LangevinThermostat nvt.CSVRThermostat nvt.GLEThermostat nvt.NHChain nvt.NHCThermostat nvt.NHCAttributeStateItem Module Contents --------------- .. py:class:: AndersenThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: select :type: jax.Array | None :value: None .. py:attribute:: annealing :type: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:class:: BerendsenThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: timecon :type: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:class:: LangevinThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: key :type: jax.Array .. py:attribute:: timecon :type: jax.Array .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: thermo(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:class:: CSVRThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: timecon :type: jax.Array .. py:attribute:: kin :type: jax.Array | None :value: None .. py:attribute:: key :type: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:class:: GLEThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: timecon :type: jax.Array .. py:attribute:: kin :type: jax.Array | None :value: None .. py:attribute:: a_p :type: jax.Array .. py:attribute:: c_p :type: jax.Array | None :value: None .. py:attribute:: ns :type: int | None :value: None .. py:attribute:: key :type: jax.Array .. py:attribute:: t :type: jax.Array | None :value: None .. py:attribute:: S :type: jax.Array | None :value: None .. py:attribute:: n_atoms :type: int | None :value: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: thermo(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:class:: NHChain(*args, **kwargs) Bases: :py:obj:`IMLCV.base.datastructures.MyPyTreeNode` Base class for dataclasses that should act like a JAX pytree node. .. py:attribute:: length :type: int :value: 3 .. py:attribute:: timestep :type: jax.Array .. py:attribute:: temp :type: jax.Array .. py:attribute:: timecon :type: jax.Array .. py:attribute:: restart_pos :type: bool :value: False .. py:attribute:: restart_vel :type: bool :value: False .. py:attribute:: pos0 :type: jax.Array | None :value: None .. py:attribute:: vel0 :type: jax.Array | None :value: None .. py:attribute:: pos :type: jax.Array | None :value: None .. py:attribute:: vel :type: jax.Array | None :value: None .. py:attribute:: masses :type: jax.Array | None :value: None .. py:attribute:: ndof :type: int :value: 0 .. py:attribute:: key :type: jax.Array .. py:method:: __post_init__() .. py:method:: set_ndof(ndof: int) -> NHChain .. py:method:: get_random_vel_therm() -> tuple[jax.Array, NHChain] .. py:method:: update(ekin, vel, G1_add) -> tuple[jax.Array, jax.Array, NHChain] .. py:method:: get_econs_correction() .. py:class:: NHCThermostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.ThermostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: kind :type: str .. py:attribute:: method :type: str .. py:attribute:: chain :type: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, G1_add=None) .. py:class:: NHCAttributeStateItem(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.iterative.StateItem` Base class for dataclasses that should act like a JAX pytree node. .. py:attribute:: attr :type: str .. py:method:: get_value(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)