Chimie Théorique » QMX

"""Structure optimization. """

import sys

import pickle

import time

from math import sqrt

from os.path import isfile

import numpy as np

from ase.parallel import rank, barrier

from ase.io.trajectory import PickleTrajectory

class Dynamics:

    """Base-class for all MD and structure optimization classes.

    Dynamics(atoms, logfile)

    atoms: Atoms object

        The Atoms object to operate on

    logfile: file object or str

        If *logfile* is a string, a file with that name will be opened.

        Use '-' for stdout.

    trajectory: Trajectory object or str

        Attach trajectory object.  If *trajectory* is a string a

        PickleTrajectory will be constructed.  Use *None* for no

        trajectory.

    """

    def __init__(self, atoms, logfile, trajectory):

        self.atoms = atoms

        if rank != 0:

            logfile = None

        elif isinstance(logfile, str):

            if logfile == '-':

                logfile = sys.stdout

            else:

                logfile = open(logfile, 'a')

        self.logfile = logfile

        self.observers = []

        self.nsteps = 0

        if trajectory is not None:

            if isinstance(trajectory, str):

                trajectory = PickleTrajectory(trajectory, 'w', atoms)

            self.attach(trajectory)

    def get_number_of_steps(self):

        return self.nsteps

    def insert_observer(self, function, position=0, interval=1, 

                        *args, **kwargs):

        """Insert an observer."""

        if not callable(function):

            function = function.write

        self.observers.insert(position, (function, interval, args, kwargs))

    def attach(self, function, interval=1, *args, **kwargs):

        """Attach callback function.

        At every *interval* steps, call *function* with arguments

        *args* and keyword arguments *kwargs*."""

        if not hasattr(function, '__call__'):

            function = function.write

        self.observers.append((function, interval, args, kwargs))

    def call_observers(self):

        for function, interval, args, kwargs in self.observers:

            if self.nsteps % interval == 0:

                function(*args, **kwargs)

class Optimizer(Dynamics):

    """Base-class for all structure optimization classes."""

    def __init__(self, atoms, restart, logfile, trajectory):

        """Structure optimizer object.

        atoms: Atoms object

            The Atoms object to relax.

        restart: str

            Filename for restart file.  Default value is *None*.

        logfile: file object or str

            If *logfile* is a string, a file with that name will be opened.

            Use '-' for stdout.

        trajectory: Trajectory object or str

            Attach trajectory object.  If *trajectory* is a string a

            PickleTrajectory will be constructed.  Use *None* for no

            trajectory.

        """

        Dynamics.__init__(self, atoms, logfile, trajectory)

        self.restart = restart

        if restart is None or not isfile(restart):

            self.initialize()

        else:

            self.read()

            barrier()

    def initialize(self):

        pass

    def run(self, fmax=0.05, steps=100000000):

        """Run structure optimization algorithm.

        This method will return when the forces on all individual

        atoms are less than *fmax* or when the number of steps exceeds

        *steps*."""

        self.fmax = fmax

        step = 0

        while step < steps:

            f = self.atoms.get_forces()

            self.log(f)

            self.call_observers()

            if self.converged(f):

                return

            self.step(f)

            self.nsteps += 1

            step += 1

    def converged(self, forces=None):

        """Did the optimization converge?"""

        if forces is None:

            forces = self.atoms.get_forces()

        return (forces**2).sum(axis=1).max() < self.fmax**2

    def log(self, forces):

        fmax = sqrt((forces**2).sum(axis=1).max())

        e = self.atoms.get_potential_energy()

        T = time.localtime()

        if self.logfile is not None:

            name = self.__class__.__name__

            self.logfile.write('%s: %3d  %02d:%02d:%02d %15.6f %12.4f\n' %

                               (name, self.nsteps, T[3], T[4], T[5], e, fmax))

            self.logfile.flush()

    def dump(self, data):

        if rank == 0 and self.restart is not None:

            pickle.dump(data, open(self.restart, 'wb'), protocol=2)

    def load(self):

        return pickle.load(open(self.restart))

class NDPoly:

    def __init__(self, ndims=1, order=3):

        """Multivariate polynomium.

        ndims: int

            Number of dimensions.

        order: int

            Order of polynomium."""

        if ndims == 0:

            exponents = [()]

        else:

            exponents = []

            for i in range(order + 1):

                E = NDPoly(ndims - 1, order - i).exponents

                exponents += [(i,) + tuple(e) for e in E]

        self.exponents = np.array(exponents)

        self.c = None

    def __call__(self, *x):

        """Evaluate polynomial at x."""

        return np.dot(self.c, (x**self.exponents).prod(1))

    def fit(self, x, y):

        """Fit polynomium at points in x to values in y."""

        A = (x**self.exponents[:, np.newaxis]).prod(2)

        self.c = np.linalg.solve(np.inner(A, A), np.dot(A, y))

def polyfit(x, y, order=3):

    """Fit polynomium at points in x to values in y.

    With D dimensions and N points, x must have shape (N, D) and y

    must have length N."""

    p = NDPoly(len(x[0]), order)

    p.fit(x, y)

    return p