"""Berendsen NPT dynamics class."""
import numpy as np
import warnings
from ase.md.nvtberendsen import NVTBerendsen
import ase.units as units
[docs]class NPTBerendsen(NVTBerendsen):
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)
def set_taup(self, taup):
self.taup = taup
def get_taup(self):
return self.taup
def set_pressure(self, pressure=None, *, pressure_au=None,
pressure_bar=None):
self.pressure = self._process_pressure(pressure, pressure_bar,
pressure_au)
def get_pressure(self):
return self.pressure
def set_compressibility(self, *, compressibility_au):
self.compressibility = compressibility_au
def get_compressibility(self):
return self.compressibility
def set_timestep(self, timestep):
self.dt = timestep
def get_timestep(self):
return self.dt
def scale_positions_and_cell(self):
""" Do the Berendsen pressure coupling,
scale the atom position and the simulation cell."""
taupscl = self.dt / self.taup
stress = self.atoms.get_stress(voigt=False, include_ideal_gas=True)
old_pressure = -stress.trace() / 3
scl_pressure = (1.0 - taupscl * self.compressibility / 3.0 *
(self.pressure - old_pressure))
#print("old_pressure", old_pressure, self.pressure)
#print("volume scaling by:", scl_pressure)
cell = self.atoms.get_cell()
cell = scl_pressure * cell
self.atoms.set_cell(cell, scale_atoms=True)
def step(self, forces=None):
""" move one timestep forward using Berenden NPT molecular dynamics."""
NVTBerendsen.scale_velocities(self)
self.scale_positions_and_cell()
# one step velocity verlet
atoms = self.atoms
if forces is None:
forces = atoms.get_forces(md=True)
p = self.atoms.get_momenta()
p += 0.5 * self.dt * forces
if self.fix_com:
# calculate the center of mass
# momentum and subtract it
psum = p.sum(axis=0) / float(len(p))
p = p - psum
self.atoms.set_positions(
self.atoms.get_positions() +
self.dt * p / self.atoms.get_masses()[:, np.newaxis])
# We need to store the momenta on the atoms before calculating
# the forces, as in a parallel Asap calculation atoms may
# migrate during force calculations, and the momenta need to
# migrate along with the atoms. For the same reason, we
# cannot use self.masses in the line above.
self.atoms.set_momenta(p)
forces = self.atoms.get_forces(md=True)
atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * forces)
return forces
def _process_pressure(self, pressure, pressure_au):
"""Handle that pressure can be specified in multiple units.
For at least a transition period, Berendsen NPT dynamics in ASE can
have the pressure specified in either bar or atomic units (eV/Å^3).
Two parameters:
pressure: None or float
The original pressure specification in bar.
A warning is issued if this is not None.
pressure_au: None or float
Pressure in ev/Å^3.
Exactly one of the two pressure parameters must be different from
None, otherwise an error is issued.
Return value: Pressure in eV/Å^3.
"""
if (pressure is not None) + (pressure_au is not None) != 1:
raise TypeError("Exactly one of the parameters 'pressure',"
+ " and 'pressure_au' must"
+ " be given")
if pressure is not None:
w = ("The 'pressure' parameter is deprecated, please"
+ " specify the pressure in atomic units (eV/Å^3)"
+ " using the 'pressure_au' parameter.")
warnings.warn(FutureWarning(w))
return pressure * (1e5 * units.Pascal)
else:
return pressure_au
class Inhomogeneous_NPTBerendsen(NPTBerendsen):
"""Berendsen (constant N, P, T) molecular dynamics.
This dynamics scale the velocities and volumes to maintain a constant
pressure and temperature. The size of the unit cell is allowed to change
independently in the three directions, but the angles remain constant.
Usage: NPTBerendsen(atoms, timestep, temperature, taut, pressure, taup)
atoms
The list of atoms.
timestep
The time step.
temperature
The desired temperature, in Kelvin.
taut
Time constant for Berendsen temperature coupling.
fixcm
If True, the position and momentum of the center of mass is
kept unperturbed. Default: True.
pressure
The desired pressure, in bar (1 bar = 1e5 Pa).
taup
Time constant for Berendsen pressure coupling.
compressibility
The compressibility of the material, water 4.57E-5 bar-1, in bar-1
mask
Specifies which axes participate in the barostat. Default (1, 1, 1)
means that all axes participate, set any of them to zero to disable
the barostat in that direction.
"""
def __init__(self, atoms, timestep, temperature=None,
*, temperature_K=None,
taut=0.5e3 * units.fs, pressure=None,
pressure_au=None, taup=1e3 * units.fs,
compressibility=None, compressibility_au=None,
mask=(1, 1, 1), fixcm=True, trajectory=None,
logfile=None, loginterval=1):
NPTBerendsen.__init__(self, atoms, timestep, temperature=temperature,
temperature_K=temperature_K,
taut=taut, taup=taup, pressure=pressure,
pressure_au=pressure_au,
compressibility=compressibility,
compressibility_au=compressibility_au,
fixcm=fixcm, trajectory=trajectory,
logfile=logfile, loginterval=loginterval)
self.mask = mask
def scale_positions_and_cell(self):
""" Do the Berendsen pressure coupling,
scale the atom position and the simulation cell."""
taupscl = self.dt * self.compressibility / self.taup / 3.0
stress = - self.atoms.get_stress(include_ideal_gas=True)
if stress.shape == (6,):
stress = stress[:3]
elif stress.shape == (3, 3):
stress = [stress[i][i] for i in range(3)]
else:
raise ValueError('Cannot use a stress tensor of shape ' +
str(stress.shape))
pbc = self.atoms.get_pbc()
scl_pressurex = 1.0 - taupscl * (self.pressure - stress[0]) \
* pbc[0] * self.mask[0]
scl_pressurey = 1.0 - taupscl * (self.pressure - stress[1]) \
* pbc[1] * self.mask[1]
scl_pressurez = 1.0 - taupscl * (self.pressure - stress[2]) \
* pbc[2] * self.mask[2]
cell = self.atoms.get_cell()
cell = np.array([scl_pressurex * cell[0],
scl_pressurey * cell[1],
scl_pressurez * cell[2]])
self.atoms.set_cell(cell, scale_atoms=True)