- class matlantis_features.features.md.ase_integrators.NPTIntegrator(timestep: float, temperature: float, pressure: float, ttime: float, pfactor: float, mask: Optional[ndarray] = None, hydrostatic_strain: bool = False)#
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Bases:
ASEIntegrator
Nose-Hoover/Parrinello-Rahman dynamics integrator generating NPT ensemble, using the ASE backend.
Methods
__init__
(timestep, temperature, pressure, …)Create the Nose-Hoover/Parrinello-Rahman dynamics integrator.
create_ase_dynamics
(atoms)Create the ASE’s Dynamics object.
set_temperature
(value)Set the target temperature of integrator.
- __init__(timestep: float, temperature: float, pressure: float, ttime: float, pfactor: float, mask: Optional[ndarray] = None, hydrostatic_strain: bool = False)#
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Create the Nose-Hoover/Parrinello-Rahman dynamics integrator.
- Parameters
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timestep (float) – Integration time step in fs unit.
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temperature (float) – Target temperature of the integrator in K unit.
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pressure (float) – Target pressure in eV/Angstrom^3 unit.
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ttime (float) – Characteristic timescale of the thermostat, in fs units.
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pfactor (float) – A constant in the barostat differential equation.
If a characteristic barostat timescale of ptime is desired,
set pfactor to ptime^2 * B (where ptime is in units matching eV, Angstrom, u;
and B is the Bulk Modulus, given in eV/Angstrom^3). -
mask (np.ndarray or None, optional) – A 3×3 array indicating if the system can change size along the three Cartesian axes.
Defaults to None. -
hydrostatic_strain (bool, optional) – Constrain the cell by only allowing hydrostatic deformation.
The virial tensor is replaced by np.diag([np.trace(virial)]*3). Defaults to False.
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- create_ase_dynamics(atoms: Atoms) Dynamics #
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Create the ASE’s Dynamics object.
- Parameters
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atoms (Atoms) – ASE’s Atoms object containing the system to simulate.
- Returns
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ASE’s Dynamics object.
- Return type
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Dynamics
- set_temperature(value: float) None #
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Set the target temperature of integrator.
If this integrator does not support temperature control,
this method raises the NotImplementedError exception.- Parameters
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value (float) – Temperature in K unit.
Resource Library
matlantis_features.features.md.ase_integrators.NPTIntegrator