Source code for ase.optimize.berny

import logging

from ase.optimize.optimize import Optimizer
from ase.units import Ha, Bohr

[docs]class Berny(Optimizer): def __init__(self, atoms, restart=None, logfile='-', trajectory=None, master=None, dihedral=True): """Berny optimizer. This is a light ASE wrapper around the ``Berny`` optimizer from Pyberny_. It is based on a redundant set of internal coordinates, and as such is best suited for optimizing covalently bonded molecules. It does not support periodic boundary conditions. You can find more information on the Pyberny_ website. This optimizer is experimental, and while it can be quite efficient when it works, it can sometimes fail entirely. These issues are most likely related to almost linear bonding angles. For context, see the discussions `here <>`__ and `here <>`__. .. _Pyberny: Parameters: atoms: Atoms object The Atoms object to relax. restart: string Pickle file used to store internal state. If set, file with such a name will be searched and internal state 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. dihedral: boolean Defaults to True, which means that dihedral angles will be used. """ from berny import Berny as _Berny, Geometry from berny.berny import BernyAdapter self._restart_data = None # Optimizer.__init__() may overwrite Optimizer.__init__(self, atoms, restart, logfile, trajectory, master) geom = Geometry(atoms.get_chemical_symbols(), atoms.positions) self._berny = _Berny( geom, debug=True, restart=self._restart_data, maxsteps=10000000000, # TODO copied from ase.optimize.Optimizer gradientmax=0., gradientrms=0., stepmax=0., steprms=0., dihedral=dihedral, ) # override the default logger to alower per-instance logfile log = logging.getLogger('{}.{}'.format(__name__, id(self))) log.addHandler(logging.StreamHandler(self.logfile)) self._berny._log = BernyAdapter(log, self._berny._log_extra) # Berny yields the initial geometry the first time because it is # typically used as a generator, see berny.optimize() next(self._berny) def step(self, f=None): if f is None: f = self.atoms.get_forces() energy = self.atoms.get_potential_energy() gradients = -self.atoms.get_forces() debug = self._berny.send((energy / Ha, gradients / Ha * Bohr)) self.dump(debug) geom = next(self._berny) self.atoms.positions[:] = geom.coords def read(self): self._restart_data = self.load()