Python optimize.Optimizer类代码示例

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 maxstep=0.04, master=None):
        """BFGS optimizer.

        Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        logfile: file object or str
            If *logfile* is a string, a file with that name will be opened.
            Use '-' for stdout.

        maxstep: float
            Used to set the maximum distance an atom can move per
            iteration (default value is 0.04 Å).

        master: boolean
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.
        """
        if maxstep > 1.0:
            warnings.warn('You are using a much too large value for '
                          'the maximum step size: %.1f Å' % maxstep)
        self.maxstep = maxstep

        Optimizer.__init__(self, atoms, restart, logfile, trajectory, master)

    def __init__(self, atoms, logfile="-", trajectory=None, callback_always=False, alpha=70.0, master=None):
        """Initialize object

        Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        logfile: file object or str
            If *logfile* is a string, a file with that name will be opened.
            Use '-' for stdout.
        
        callback_always: book
            Should the callback be run after each force call (also in the
            linesearch)

        alpha: float
            Initial guess for the Hessian (curvature of energy surface). A
            conservative value of 70.0 is the default, but number of needed
            steps to converge might be less if a lower value is used. However,
            a lower value also means risk of instability.

        master: boolean
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.
        """
        restart = None
        Optimizer.__init__(self, atoms, restart, logfile, trajectory, master)
        self.force_calls = 0
        self.callback_always = callback_always
        self.H0 = alpha

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 dt=0.1, maxmove=0.2, dtmax=1.0, Nmin=5, finc=1.1, fdec=0.5,
                 astart=0.1, fa=0.99, a=0.1, master=None, downhill_check=False,
                 position_reset_callback=None, force_consistent=None):
        """Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        logfile: file object or str
            If *logfile* is a string, a file with that name will be opened.
            Use '-' for stdout.

        master: boolean
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.

        downhill_check: boolean
            Downhill check directly compares potential energies of subsequent
            steps of the FIRE algorithm rather than relying on the current
            product v*f that is positive if the FIRE dynamics moves downhill.
            This can detect numerical issues where at large time steps the step
            is uphill in energy even though locally v*f is positive, i.e. the
            algorithm jumps over a valley because of a too large time step.

        position_reset_callback: function(atoms, r, e, e_last)
            Function that takes current *atoms* object, an array of position
            *r* that the optimizer will revert to, current energy *e* and
            energy of last step *e_last*. This is only called if e > e_last.

        force_consistent: boolean or None
            Use force-consistent energy calls (as opposed to the energy
            extrapolated to 0 K).  By default (force_consistent=None) uses
            force-consistent energies if available in the calculator, but
            falls back to force_consistent=False if not.  Only meaningful
            when downhill_check is True.
        """
        Optimizer.__init__(self, atoms, restart, logfile, trajectory,
                           master, force_consistent=force_consistent)

        self.dt = dt
        self.Nsteps = 0
        self.maxmove = maxmove
        self.dtmax = dtmax
        self.Nmin = Nmin
        self.finc = finc
        self.fdec = fdec
        self.astart = astart
        self.fa = fa
        self.a = a
        self.downhill_check = downhill_check
        self.position_reset_callback = position_reset_callback

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 dt=None, master=None):
        """Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        maxstep: float
            Used to set the maximum distance an atom can move per
            iteration (default value is 0.2 Angstroms).

        logfile: string
            Text file used to write summary information.

        master: boolean
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.
        """
        Optimizer.__init__(self, atoms, restart, logfile, trajectory, master)

        if dt is not None:
            self.dt = dt

    def __init__(self, atoms, restart=None, logfile='-', maxstep=.2,
                 trajectory=None, c1=0.23, c2=0.46, alpha=10.0, stpmax=50.0,
                 master=None, force_consistent=None):
        """Optimize atomic positions in the BFGSLineSearch algorithm, which
        uses both forces and potential energy information.

        Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        maxstep: float
            Used to set the maximum distance an atom can move per
            iteration (default value is 0.2 Angstroms).

        logfile: file object or str
            If *logfile* is a string, a file with that name will be opened.
            Use '-' for stdout.

        master: boolean
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.

        force_consistent: boolean or None
            Use force-consistent energy calls (as opposed to the energy
            extrapolated to 0 K).  By default (force_consistent=None) uses
            force-consistent energies if available in the calculator, but
            falls back to force_consistent=False if not.
        """
        self.maxstep = maxstep
        self.stpmax = stpmax
        self.alpha = alpha
        self.H = None
        self.c1 = c1
        self.c2 = c2
        self.force_calls = 0
        self.function_calls = 0
        self.r0 = None
        self.g0 = None
        self.e0 = None
        self.load_restart = False
        self.task = 'START'
        self.rep_count = 0
        self.p = None
        self.alpha_k = None
        self.no_update = False
        self.replay = False

        Optimizer.__init__(self, atoms, restart, logfile, trajectory,
                           master, force_consistent)

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 maxstep=None, memory=100, damping=1.0, alpha=70.0,
                 use_line_search=False):
        """
        Parameters:

        restart: string
            Pickle file used to store vectors for updating the inverse of
            Hessian matrix. If set, file with such a name will be searched
            and information stored will be used, if the file exists.

        logfile: string
            Where should output go. None for no output, '-' for stdout.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        maxstep: float
            How far is a single atom allowed to move. This is useful for DFT
            calculations where wavefunctions can be reused if steps are small.
            Default is 0.04 Angstrom.

        memory: int
            Number of steps to be stored. Default value is 100. Three numpy
            arrays of this length containing floats are stored.

        damping: float
            The calculated step is multiplied with this number before added to
            the positions.

        alpha: float
            Initial guess for the Hessian (curvature of energy surface). A
            conservative value of 70.0 is the default, but number of needed
            steps to converge might be less if a lower value is used. However,
            a lower value also means risk of instability.
            
        """
        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

        if maxstep is not None:
            if maxstep > 1.0:
                raise ValueError('You are using a much too large value for ' +
                                 'the maximum step size: %.1f Angstrom' %
                                 maxstep)
            self.maxstep = maxstep
        else:
            self.maxstep = 0.04

        self.memory = memory
        self.H0 = 1. / alpha  # Initial approximation of inverse Hessian
                            # 1./70. is to emulate the behaviour of BFGS
                            # Note that this is never changed!
        self.damping = damping
        self.use_line_search = use_line_search
        self.p = None
        self.function_calls = 0
        self.force_calls = 0

    def __init__(self, atoms, logfile='-', trajectory=None,
                 callback_always=False):
        """Parameters:

        callback_always: book
            Should the callback be run after each force call (also in the
            linesearch)
        """
        restart = None
        Optimizer.__init__(self, atoms, restart, logfile, trajectory)
        self.function_calls = 0
        self.callback_always = callback_always

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 dt=0.1, maxmove=0.2, dtmax=1.0, Nmin=5, finc=1.1, fdec=0.5,
                 astart=0.1, fa=0.99, a=0.1, theta=0.1, master=None,
                 precon=None, use_armijo=True, variable_cell=False):
        """
        Preconditioned version of the FIRE optimizer

        Parameters:

        atoms: Atoms object
            The Atoms object to relax.

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.

        trajectory: string
            Pickle file used to store trajectory of atomic movement.

        logfile: file object or str
            If *logfile* is a string, a file with that name will be opened.
            Use '-' for stdout.

        master: bool
            Defaults to None, which causes only rank 0 to save files.  If
            set to true,  this rank will save files.

        variable_cell: bool
            If True, wrap atoms in UnitCellFilter to relax cell and positions.

        In time this implementation is expected to replace
        ase.optimize.fire.FIRE.
        """
        if variable_cell:
            atoms = UnitCellFilter(atoms)
        Optimizer.__init__(self, atoms, restart, logfile, trajectory, master)

        self.dt = dt
        self.Nsteps = 0
        self.maxmove = maxmove
        self.dtmax = dtmax
        self.Nmin = Nmin
        self.finc = finc
        self.fdec = fdec
        self.astart = astart
        self.fa = fa
        self.a = a
        self.theta = theta
        self.precon = precon
        self.use_armijo = use_armijo

 def __init__(self, atoms, restart=None, logfile=None, trajectory=None,
              seed=None,
              verbose=False):
     Optimizer.__init__(self, atoms, restart, logfile, trajectory)
     atoms.get_forces()
     atoms.get_potential_energy()
     if seed is None:
         seed = np.random.randint(0, 2 ** 31)
     self.verbose = verbose
     self.random_state = RandomState(seed)
     self.starting_atoms = dc(atoms)
     self.traj = [dc(atoms)]
     self.pe = []
     self.metadata = {'seed': seed}

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 dt=0.1, maxmove=0.2, dtmax=1.0, Nmin=5, finc=1.1, fdec=0.5,
                 astart=0.1, fa=0.99, a=0.1):
        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

        self.dt = dt
        self.Nsteps = 0
        self.maxmove = maxmove
        self.dtmax = dtmax
        self.Nmin = Nmin
        self.finc = finc
        self.fdec = fdec
        self.astart = astart
        self.fa = fa
        self.a = a

    def __init__(self, atoms, logfile='-', trajectory=None):
        Optimizer.__init__(self, atoms, None, logfile, trajectory)

        self.control = atoms.get_control()

        # Make a header for the log
        if self.logfile is not None:
            l = ''
            if isinstance(self.control, DimerControl):
                l = 'MinModeTranslate: STEP      TIME          ENERGY    ' + \
                    'MAX-FORCE     STEPSIZE    CURVATURE  ROT-STEPS\n'
            self.logfile.write(l)
            self.logfile.flush()

        # Load the relevant parameters from control
        self.cg_on = self.control.get_parameter('cg_translation')
        self.trial_step = self.control.get_parameter('trial_trans_step')
        self.max_step = self.control.get_parameter('maximum_translation')

        # Start conjugate gradient
        if self.cg_on:
            self.cg_init = True

    def __init__(self, atoms, restart=None, logfile='-', maxstep=.2,
                 trajectory=None, c1=.23, c2=0.46, alpha=10., stpmax=50.,
                 use_free_energy=True):
        """Minimize a function using the BFGS algorithm.

        Notes:

            Optimize the function, f, whose gradient is given by fprime
            using the quasi-Newton method of Broyden, Fletcher, Goldfarb,
            and Shanno (BFGS) See Wright, and Nocedal 'Numerical
            Optimization', 1999, pg. 198.

        *See Also*:

          scikits.openopt : SciKit which offers a unified syntax to call
                            this and other solvers.

        """
        self.maxstep = maxstep
        self.stpmax = stpmax
        self.alpha = alpha
        self.H = None
        self.c1 = c1
        self.c2 = c2
        self.force_calls = 0
        self.function_calls = 0
        self.r0 = None
        self.g0 = None
        self.e0 = None
        self.load_restart = False
        self.task = 'START'
        self.rep_count = 0
        self.p = None
        self.alpha_k = None
        self.no_update = False
        self.replay = False
        self.use_free_energy = use_free_energy

        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

    def __init__(self, atoms, restart=None, logfile='-', maxstep=.2,
                 trajectory=None, c1=0.23, c2=0.46, alpha=10.0, stpmax=50.0):
        """Optimize atomic positions in the BFGSLineSearch algorithm, which
        uses both forces and potential energy information.

        Parameters:

        restart: string
            Pickle file used to store hessian matrix. If set, file with
            such a name will be searched and hessian matrix stored will
            be used, if the file exists.
        trajectory: string
            Pickle file used to store trajectory of atomic movement.
        maxstep: float
            Used to set the maximum distance an atom can move per
            iteration (default value is 0.2 Angstroms).
        logfile: string
            Text file used to write summary information.
        """
        self.maxstep = maxstep
        self.stpmax = stpmax
        self.alpha = alpha
        self.H = None
        self.c1 = c1
        self.c2 = c2
        self.force_calls = 0
        self.function_calls = 0
        self.r0 = None
        self.g0 = None
        self.e0 = None
        self.load_restart = False
        self.task = 'START'
        self.rep_count = 0
        self.p = None
        self.alpha_k = None
        self.no_update = False
        self.replay = False

        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

    def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
                 fmax=None, converged=None,
                hessianupdate='BFGS',hessian=None,forcemin=True,
                verbosity=None,maxradius=None,
                diagonal=20.,radius=None,
                transitionstate = False):
            
        Optimizer.__init__(self, atoms, restart, logfile, trajectory)

        self.eps = 1e-12
        self.hessianupdate = hessianupdate
        self.forcemin = forcemin
        self.verbosity = verbosity
        self.diagonal = diagonal

        self.atoms = atoms

        n = len(self.atoms) * 3
        if radius is None: 
                self.radius = 0.05*np.sqrt(n)/10.0
        else:
                self.radius = radius

        if maxradius is None: 
                self.maxradius = 0.5*np.sqrt(n)
        else:
                self.maxradius = maxradius
                
        # 0.01 < radius < maxradius
        self.radius = max(min( self.radius, self.maxradius ), 0.0001)

        self.transitionstate = transitionstate

        # check if this is a nudged elastic band calculation
        if hasattr(atoms,'springconstant'): 
                self.forcemin=False

        self.t0 = time.time() 

 def __init__(self, atoms, restart=None, logfile=None, trajectory=None,
              seed=None,
              verbose=False):
     Optimizer.__init__(self, atoms, restart, logfile, trajectory=None)
     atoms.get_forces()
     atoms.get_potential_energy()
     if seed is None:
         seed = np.random.randint(0, 2 ** 31)
     self.verbose = verbose
     self.random_state = RandomState(seed)
     self.starting_atoms = dc(atoms)
     self.pe = []
     self.metadata = {'seed': seed}
     self.traj = [dc(atoms)]
     print(self.traj[0].get_momenta())
     if trajectory is not None:
         self.trajectory = Trajectory(trajectory, mode='w')
         self.trajectory.write(self.traj[-1])
         if self.verbose:
             print('Trajectory written', len(self.traj))
     else:
         self.trajectory = None
     if verbose:
         print('trajectory file', self.trajectory)