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import argparse
import traceback
from math import pi
from time import time
import numpy as np
import ase.db
import ase.optimize
from ase.calculators.emt import EMT
from ase.io import Trajectory
all_optimizers = ase.optimize.__all__ + ['PreconLBFGS', 'PreconFIRE',
'SciPyFminCG', 'SciPyFminBFGS']
all_optimizers.remove('QuasiNewton')
all_optimizers.remove('RestartError')
def get_optimizer(name):
# types: (str) -> ase.optimize.Optimizer
if name.startswith('Precon'):
import ase.optimize.precon as precon
return getattr(precon, name)
if name.startswith('SciPy'):
import ase.optimize.sciopt as sciopt
return getattr(sciopt, name)
return getattr(ase.optimize, name)
class Wrapper:
"""Atoms-object wrapper that can count number of moves."""
def __init__(self, atoms, gridspacing=0.2, eggbox=0.0):
# types: (Atoms, float, float) -> None
self.t0 = time()
self.texcl = 0.0
self.nsteps = 0
self.atoms = atoms
self.ready = False
self.pos = None # type: np.ndarray
self.eggbox = eggbox
if eggbox:
# Find small unit cell for grid-points
h = []
for axis in atoms.get_cell(complete=True):
L = np.linalg.norm(axis)
n = int(L / gridspacing)
h.append(axis / n)
self.x = np.linalg.inv(h)
else:
self.x = None
def get_potential_energy(self, force_consistent=False):
t1 = time()
e = self.atoms.get_potential_energy(force_consistent)
if self.eggbox:
# Add egg-box error:
s = np.dot(self.atoms.positions, self.x)
e += np.cos(2 * pi * s).sum() * self.eggbox / 6
t2 = time()
self.texcl += t2 - t1
if not self.ready:
self.nsteps += 1
self.ready = True
return e
def get_forces(self):
t1 = time()
f = self.atoms.get_forces()
if self.eggbox:
# Add egg-box error:
s = np.dot(self.atoms.positions, self.x)
f += np.dot(np.sin(2 * pi * s),
self.x.T) * (2 * pi * self.eggbox / 6)
t2 = time()
self.texcl += t2 - t1
if not self.ready:
self.nsteps += 1
self.ready = True
return f
def set_positions(self, pos):
if self.pos is not None and abs(pos - self.pos).max() > 1e-15:
self.ready = False
if self.nsteps == 200:
raise RuntimeError('Did not converge!')
self.pos = pos
self.atoms.set_positions(pos)
def get_positions(self):
return self.atoms.get_positions()
def get_calculator(self):
return self.atoms.calc
def __len__(self):
return len(self.atoms)
def __getattr__(self, name):
return self.atoms.__getattribute__(name)
def run_test(atoms, optimizer, tag, fmax=0.02, eggbox=0.0):
"""Optimize atoms with optimizer."""
wrapper = Wrapper(atoms, eggbox=eggbox)
relax = optimizer(wrapper, logfile=tag + '.log')
relax.attach(Trajectory(tag + '.traj', 'w', atoms=atoms))
tincl = -time()
error = ''
try:
relax.run(fmax=fmax, steps=10000000)
except Exception as x:
wrapper.nsteps = float('inf')
error = '{}: {}'.format(x.__class__.__name__, x)
tb = traceback.format_exc()
with open(tag + '.err', 'w') as fd:
fd.write('{}\n{}\n'.format(error, tb))
tincl += time()
return error, wrapper.nsteps, wrapper.texcl, tincl
def test_optimizer(systems, optimizer, calculator, prefix='', db=None,
eggbox=0.0):
"""Test optimizer on systems."""
for name, atoms in systems:
if db is not None:
optname = optimizer.__name__
id = db.reserve(optimizer=optname, name=name)
if id is None:
continue
atoms = atoms.copy()
tag = '{}{}-{}'.format(prefix, optname, name)
atoms.calc = calculator(txt=tag + '.txt')
error, nsteps, texcl, tincl = run_test(atoms, optimizer, tag,
eggbox=eggbox)
if db is not None:
db.write(atoms,
id=id,
optimizer=optname,
name=name,
error=error,
n=nsteps,
t=texcl,
T=tincl,
eggbox=eggbox)
def main():
parser = argparse.ArgumentParser(
description='Test ASE optimizers')
parser.add_argument('systems', help='File containing test systems.')
parser.add_argument('optimizer', nargs='*',
help='Optimizer name(s). Choose from: {}. '
.format(', '.join(all_optimizers)) +
'Default is all optimizers.')
parser.add_argument('-e', '--egg-box', type=float, default=0.0,
help='Fake egg-box error in eV.')
args = parser.parse_args()
systems = [(row.name, row.toatoms())
for row in ase.db.connect(args.systems).select()]
db = ase.db.connect('results.db')
if not args.optimizer:
args.optimizer = all_optimizers
for opt in args.optimizer:
print(opt)
optimizer = get_optimizer(opt)
test_optimizer(systems, optimizer, EMT, db=db, eggbox=args.egg_box)
if __name__ == '__main__':
main()
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