Chimie Théorique » QMX

"""Berendsen NPT dynamics class."""

import numpy as np

#from ase.md import MolecularDynamics

from ase.md.nvtberendsen import NVTBerendsen

import ase.units as units

#import math

class NPTBerendsen(NVTBerendsen):

    """Berendsen (constant N, P, T) molecular dynamics.

    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):

        NVTBerendsen.__init__(self, atoms, timestep, temperature, taut, fixcm,

                              trajectory,

                              logfile, loginterval)

        self.taup = taup

        self.pressure = pressure

        self.compressibility = compressibility

    def set_taup(self, taut):

        self.taut = taut

    def get_taup(self):

        return self.taut

    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 positon and the simulation cell."""

        taupscl = self.dt / self.taup

        stress = self.atoms.get_stress()

        old_pressure = self.atoms.get_isotropic_pressure(stress)

        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()

        positions = self.atoms.get_positions()

        cell = scl_pressure * cell

        positions = scl_pressure * positions

        self.atoms.set_cell(cell, scale_atoms=False)

        self.atoms.set_positions(positions)

        return

    def step(self, f):

        """ 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

        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