npt === .. py:module:: npt .. autoapi-nested-parse:: Barostats Classes ------- .. autoapisummary:: npt.TBCombination npt.McDonaldBarostat npt.BerendsenBarostat npt.LangevinBarostat npt.MTKBarostat npt.PRBarostat npt.TadmorBarostat npt.MTKAttributeStateItem Module Contents --------------- .. py:class:: TBCombination(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` Specialized Verlet hook. This is mainly used for the implementation of thermostats and barostats. .. py:attribute:: name :type: str .. py:attribute:: temp :type: jax.Array .. py:attribute:: press :type: jax.Array .. py:attribute:: thermostat :type: IMLCV.new_yaff.verlet.ThermostatHook .. py:attribute:: barostat :type: IMLCV.new_yaff.verlet.BarostatHook .. py:attribute:: step_thermo :type: jax.Array .. py:attribute:: step_baro :type: jax.Array .. py:attribute:: baro_expects_call :type: bool .. py:attribute:: thermo_expects_call :type: bool .. py:attribute:: chainvel0 :type: jax.Array | None :value: None .. py:attribute:: G1_add :type: jax.Array | None :value: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: __call__(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: verify() .. py:class:: McDonaldBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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:: amp :type: jax.Array .. py:attribute:: dim :type: int | None :value: 3 .. py:attribute:: key :type: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:class:: BerendsenBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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_press :type: jax.Array .. py:attribute:: beta :type: jax.Array .. py:attribute:: anisotropic :type: bool .. py:attribute:: vol_constraint :type: bool .. py:attribute:: mass_press :type: jax.Array | None :value: None .. py:attribute:: cell :type: jax.Array | None :value: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:class:: LangevinBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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:attribute:: anisotropic :type: bool .. py:attribute:: vol_constraint :type: bool .. py:attribute:: vel_press :type: jax.Array .. py:attribute:: timestep_press :type: jax.Array | None :value: None .. py:attribute:: mass_press :type: 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. .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0) .. py:method:: getR() .. py:class:: MTKBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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:: cell :type: jax.Array | None :value: None .. py:attribute:: timecon :type: jax.Array .. py:attribute:: anisotropic :type: bool .. py:attribute:: vol_constraint :type: bool .. py:attribute:: vel_press :type: jax.Array .. py:attribute:: baro_thermo :type: IMLCV.new_yaff.nvt.NHCThermostat | None :value: None .. py:attribute:: timecon_press :type: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0) .. py:method:: add_press_cont() .. py:method:: _compute_ekin_baro() .. py:class:: PRBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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_press :type: jax.Array .. py:attribute:: anisotropic :type: bool .. py:attribute:: vol_constraint :type: bool .. py:attribute:: mass_press :type: jax.Array | None :value: None .. py:attribute:: cell :type: jax.Array | None :value: None .. py:attribute:: baro_thermo :type: IMLCV.new_yaff.nvt.NHCThermostat | None :value: None .. py:attribute:: P :type: jax.Array | None :value: None .. py:attribute:: S_ani :type: jax.Array | None :value: None .. py:attribute:: cellinv0 :type: jax.Array | None :value: None .. py:attribute:: vol0 :type: jax.Array | None :value: None .. py:attribute:: Sigma :type: jax.Array | None :value: None .. py:attribute:: vel_press :type: jax.Array | None :value: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0) .. py:method:: add_press_cont() .. py:method:: _compute_ekin_baro() .. py:class:: TadmorBarostat(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.verlet.BarostatHook` 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_press :type: jax.Array | float :value: 41341.37333664682 .. py:attribute:: anisotropic :type: bool .. py:attribute:: vol_constraint :value: False .. py:attribute:: mass_press :type: jax.Array | float | None :value: None .. py:attribute:: baro_thermo :type: IMLCV.new_yaff.nvt.NHCThermostat | None :value: None .. py:attribute:: vel_press :type: jax.Array | None :value: None .. py:attribute:: cell :type: jax.Array | None :value: None .. py:attribute:: cellinv0 :type: jax.Array | None :value: None .. py:attribute:: Strans :type: jax.Array | None :value: None .. py:attribute:: Vol0 :type: jax.Array | None :value: None .. py:attribute:: key :type: 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 .. py:method:: init(iterative: IMLCV.new_yaff.verlet.VerletIntegrator) .. py:method:: pre(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: post(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0=None) .. py:method:: baro(iterative: IMLCV.new_yaff.verlet.VerletIntegrator, chainvel0) .. py:method:: add_press_cont() .. py:method:: _compute_ekin_baro() .. py:method:: _compute_angular_tensor(pos, vel, masses) .. py:class:: MTKAttributeStateItem(*args, **kwargs) Bases: :py:obj:`IMLCV.new_yaff.iterative.StateItem` Base class for dataclasses that should act like a JAX pytree node. .. py:attribute:: key :type: str :value: 'MTKattr' .. py:attribute:: attr :type: str .. py:method:: get_value(iterative: IMLCV.new_yaff.verlet.VerletIntegrator)