def __init__(self,
atoms,
timestep,
temperature,
taut=0.5e3 * units.fs,
pressure=1.01325,
taup=1e3 * units.fs,
compressibility=4.57e-5,
fixcm=True,
trajectory=None,
logfile=None,
loginterval=1,
append_trajectory=False):
NVTBerendsen.__init__(self,
atoms,
timestep,
temperature,
taut,
fixcm,
trajectory,
logfile,
loginterval,
append_trajectory=append_trajectory)
self.taup = taup
self.pressure = pressure
self.compressibility = compressibility
def __init__(self, atoms, timestep, temperature, taut, fixcm=True,
trajectory=None, **kwargs):
NVTBerendsen.__init__(self, atoms, timestep, temperature, taut,
fixcm, trajectory)
OTF.__init__(self, **kwargs)
self.md_engine = 'NVTBerendsen'
def __init__(self, atoms, timestep, temperature, taut=0.5e3 *
units.fs, pressure=1.01325, taup=1e3 * units.fs,
compressibility=4.57e-5, fixcm=True, trajectory=None,
logfile=None, loginterval=1):
NVTBerendsen.__init__(self, atoms, timestep, temperature,
taut, fixcm, trajectory, logfile,
loginterval)
self.taup = taup
self.pressure = pressure
self.compressibility = compressibility
def set_initial_velocities(self, distribution, energy):
distribution(self.atoms, energy)
try:
os.remove(self.traj)
except:
pass
try:
os.remove(self._log)
except:
pass
NVTBerendsen.__init__(self,
atoms=self.atoms,
timestep=self.dt,
trajectory=self.traj,
loginterval=1,
logfile=self._log,
temperature=self.target_temperature,
taut=self.tau,
append_trajectory=False)
self.update_properties()
def __init__(self, atoms, timestep, temperature=None,
*, temperature_K=None, pressure=None, pressure_au=None,
taut=0.5e3 * units.fs, taup=1e3 * units.fs,
compressibility=None, compressibility_au=None, fixcm=True,
trajectory=None,
logfile=None, loginterval=1, append_trajectory=False):
"""Berendsen (constant N, P, T) molecular dynamics.
This dynamics scale the velocities and volumes to maintain a constant
pressure and temperature. The shape of the simulation cell is not
altered, if that is desired use Inhomogenous_NPTBerendsen.
Parameters:
atoms: Atoms object
The list of atoms.
timestep: float
The time step in ASE time units.
temperature: float
The desired temperature, in Kelvin.
temperature_K: float
Alias for ``temperature``.
pressure: float (deprecated)
The desired pressure, in bar (1 bar = 1e5 Pa). Deprecated,
use ``pressure_au`` instead.
pressure: float
The desired pressure, in atomic units (eV/Å^3).
taut: float
Time constant for Berendsen temperature coupling in ASE
time units. Default: 0.5 ps.
taup: float
Time constant for Berendsen pressure coupling. Default: 1 ps.
compressibility: float (deprecated)
The compressibility of the material, in bar-1. Deprecated,
use ``compressibility_au`` instead.
compressibility_au: float
The compressibility of the material, in atomic units (Å^3/eV).
fixcm: bool (optional)
If True, the position and momentum of the center of mass is
kept unperturbed. Default: True.
trajectory: Trajectory object or str (optional)
Attach trajectory object. If *trajectory* is a string a
Trajectory will be constructed. Use *None* for no
trajectory.
logfile: file object or str (optional)
If *logfile* is a string, a file with that name will be opened.
Use '-' for stdout.
loginterval: int (optional)
Only write a log line for every *loginterval* time steps.
Default: 1
append_trajectory: boolean (optional)
Defaults to False, which causes the trajectory file to be
overwriten each time the dynamics is restarted from scratch.
If True, the new structures are appended to the trajectory
file instead.
"""
NVTBerendsen.__init__(self, atoms, timestep, temperature=temperature,
temperature_K=temperature_K,
taut=taut, fixcm=fixcm, trajectory=trajectory,
logfile=logfile, loginterval=loginterval,
append_trajectory=append_trajectory)
self.taup = taup
self.pressure = self._process_pressure(pressure, pressure_au)
if compressibility is not None and compressibility_au is not None:
raise TypeError(
"Do not give both 'compressibility' and 'compressibility_au'")
if compressibility is not None:
# Specified in bar, convert to atomic units
warnings.warn(FutureWarning(
"Specify the compressibility in atomic units."))
self.set_compressibility(
compressibility_au=compressibility / (1e5 * units.Pascal))
else:
self.set_compressibility(compressibility_au=compressibility_au)
