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# Source code for ase.md.nvtberendsen

    """Berendsen NVT dynamics class."""

    import numpy as np
    from ase.md.md import MolecularDynamics
    from ase.parallel import world

    class NVTBerendsen(MolecularDynamics):
        def __init__(self, atoms, timestep, temperature=None, taut=None,
                     fixcm=True, *, temperature_K=None,
                     trajectory=None, logfile=None, loginterval=1,
                     communicator=world, append_trajectory=False):
            """Berendsen (constant N, V, T) molecular dynamics.

            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*

            taut: float
                Time constant for Berendsen temperature coupling in ASE
                time units.

            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.

            """

            MolecularDynamics.__init__(self, atoms, timestep, trajectory,
                                       logfile, loginterval,
                                       append_trajectory=append_trajectory)
            if taut is None:
                raise TypeError("Missing 'taut' argument.")
            self.taut = taut
            self.temperature = self._process_temperature(temperature,
                                                         temperature_K, 'K')

            self.fix_com = fixcm  # will the center of mass be held fixed?
            self.communicator = communicator

        def set_taut(self, taut):
            self.taut = taut

        def get_taut(self):
            return self.taut

        def set_temperature(self, temperature=None, *, temperature_K=None):
            self.temperature = self._process_temperature(temperature,
                                                         temperature_K, 'K')

        def get_temperature(self):
            return self.temperature

        def set_timestep(self, timestep):
            self.dt = timestep

        def get_timestep(self):
            return self.dt

        def scale_velocities(self):
            """ Do the NVT Berendsen velocity scaling """
            tautscl = self.dt / self.taut
            old_temperature = self.atoms.get_temperature()

            scl_temperature = np.sqrt(1.0 +
                                      (self.temperature / old_temperature - 1.0) *
                                      tautscl)
            # Limit the velocity scaling to reasonable values
            if scl_temperature > 1.1:
                scl_temperature = 1.1
            if scl_temperature < 0.9:
                scl_temperature = 0.9

            p = self.atoms.get_momenta()
            p = scl_temperature * p
            self.atoms.set_momenta(p)
            return

        def step(self, forces=None):
            """Move one timestep forward using Berenden NVT molecular dynamics."""
            self.scale_velocities()

            # 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