"""Berendsen NPT dynamics class."""
import numpy as np
from ase.md.nvtberendsen import NVTBerendsen
import ase.units as units
[docs]class NPTBerendsen(NVTBerendsen):
"""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.
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
"""
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 set_taup(self, taup):
self.taup = taup
def get_taup(self):
return self.taup
def set_pressure(self, pressure):
self.pressure = pressure
def get_pressure(self):
return self.pressure
def set_compressibility(self, compressibility):
self.compressibility = compressibility
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 * 1e-5 / units.Pascal
scl_pressure = (1.0 - taupscl * self.compressibility / 3.0 *
(self.pressure - old_pressure))
#print "old_pressure", old_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, f=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 f is None:
f = atoms.get_forces()
p = self.atoms.get_momenta()
p += 0.5 * self.dt * f
if self.fixcm:
# 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)
f = self.atoms.get_forces()
atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * f)
return f
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,
taut=0.5e3 * units.fs, pressure=1.01325, taup=1e3 * units.fs,
compressibility=4.57e-5, mask=(1, 1, 1),
fixcm=True, trajectory=None,
logfile=None, loginterval=1):
NPTBerendsen.__init__(self, atoms, timestep, temperature,
taut, pressure, taup, compressibility,
fixcm, trajectory, logfile,
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) * 1e-5 / units.Pascal
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)