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# fmt: off
import os
from typing import Any, Union
import numpy as np
from ase import Atoms
from ase.io.jsonio import read_json, write_json
from ase.parallel import parprint, world
DFTCalculator = Any
def ensemble(energy: float,
contributions: np.ndarray,
xc: str,
verbose: bool = False) -> np.ndarray:
"""Returns an array of ensemble total energies."""
ensemble = BEEFEnsemble(None, energy, contributions, xc, verbose)
return ensemble.get_ensemble_energies()
class BEEFEnsemble:
"""BEEF type ensemble error estimation."""
def __init__(self,
atoms: Union[Atoms, DFTCalculator] = None,
e: float = None,
contribs: np.ndarray = None,
xc: str = None,
verbose: bool = True):
if (atoms is not None or contribs is not None or xc is not None):
if atoms is None:
assert e is not None
assert contribs is not None
assert xc is not None
else:
if isinstance(atoms, Atoms):
calc = atoms.calc
self.atoms = atoms
else:
calc = atoms
self.atoms = calc.atoms
self.calc = calc
xc = self.calc.get_xc_functional()
self.e = e
self.contribs = contribs
self.xc = xc
self.verbose = verbose
self.done = False
if self.xc in ['BEEF-vdW', 'BEEF', 'PBE']:
self.beef_type = 'beefvdw'
elif self.xc == 'mBEEF':
self.beef_type = 'mbeef'
elif self.xc == 'mBEEF-vdW':
self.beef_type = 'mbeefvdw'
else:
raise NotImplementedError(f'No ensemble for xc = {self.xc}')
def get_ensemble_energies(self,
size: int = 2000,
seed: int = 0) -> np.ndarray:
"""Returns an array of ensemble total energies"""
self.seed = seed
if self.verbose:
parprint(self.beef_type, 'ensemble started')
if self.contribs is None:
self.contribs = self.calc.get_nonselfconsistent_energies(
self.beef_type)
self.e = self.calc.get_potential_energy(self.atoms)
if self.beef_type == 'beefvdw':
assert len(self.contribs) == 32
coefs = self.get_beefvdw_ensemble_coefs(size, seed)
elif self.beef_type == 'mbeef':
assert len(self.contribs) == 64
coefs = self.get_mbeef_ensemble_coefs(size, seed)
elif self.beef_type == 'mbeefvdw':
assert len(self.contribs) == 28
coefs = self.get_mbeefvdw_ensemble_coefs(size, seed)
self.de = np.dot(coefs, self.contribs)
self.done = True
if self.verbose:
parprint(self.beef_type, 'ensemble finished')
return self.e + self.de
def get_beefvdw_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the BEEF-vdW ensemble"""
from ase.dft.pars_beefvdw import uiOmega as omega
assert np.shape(omega) == (31, 31)
W, V, generator = self.eigendecomposition(omega, seed)
RandV = generator.randn(31, size)
for j in range(size):
v = RandV[:, j]
coefs_i = (np.dot(np.dot(V, np.diag(np.sqrt(W))), v)[:])
if j == 0:
ensemble_coefs = coefs_i
else:
ensemble_coefs = np.vstack((ensemble_coefs, coefs_i))
PBEc_ens = -ensemble_coefs[:, 30]
return (np.vstack((ensemble_coefs.T, PBEc_ens))).T
def get_mbeef_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the mBEEF ensemble"""
from ase.dft.pars_mbeef import uiOmega as omega
assert np.shape(omega) == (64, 64)
W, V, generator = self.eigendecomposition(omega, seed)
mu, sigma = 0.0, 1.0
rand = np.array(generator.normal(mu, sigma, (len(W), size)))
return (np.sqrt(2) * np.dot(np.dot(V, np.diag(np.sqrt(W))),
rand)[:]).T
def get_mbeefvdw_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the mBEEF-vdW ensemble"""
from ase.dft.pars_mbeefvdw import uiOmega as omega
assert np.shape(omega) == (28, 28)
W, V, generator = self.eigendecomposition(omega, seed)
mu, sigma = 0.0, 1.0
rand = np.array(generator.normal(mu, sigma, (len(W), size)))
return (np.sqrt(2) * np.dot(np.dot(V, np.diag(np.sqrt(W))), rand)[:]).T
def eigendecomposition(self, omega, seed=0):
_u, s, v = np.linalg.svd(omega) # unsafe: W, V = np.linalg.eig(omega)
generator = np.random.RandomState(seed)
return s, v.T, generator
def write(self, fname):
"""Write ensemble data file"""
if not fname.endswith('.bee'):
fname += '.bee'
assert self.done
if world.rank == 0:
if os.path.isfile(fname):
os.rename(fname, fname + '.old')
obj = [self.e, self.de, self.contribs, self.seed, self.xc]
with open(fname, 'w') as fd:
write_json(fd, obj)
def readbee(fname: str, all: bool = False):
if not fname.endswith('.bee'):
fname += '.bee'
with open(fname) as fd:
e, de, contribs, seed, xc = read_json(fd, always_array=False)
if all:
return e, de, contribs, seed, xc
else:
return e + de
def BEEF_Ensemble(*args, **kwargs):
import warnings
warnings.warn('Please use BEEFEnsemble instead of BEEF_Ensemble.')
return BEEFEnsemble(*args, **kwargs)
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