def test_standardcomparator():
from ase.ga.standard_comparators import (InteratomicDistanceComparator,
EnergyComparator,
RawScoreComparator,
SequentialComparator)
from ase import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.ga import set_raw_score
a1 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.5, 0, 0], [1.5, 1.5, 0]])
a2 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.4, 0, 0], [1.5, 1.5, 0]])
e1 = 1.0
e2 = 0.8
a1.set_calculator(SinglePointCalculator(a1, energy=e1))
a2.set_calculator(SinglePointCalculator(a2, energy=e2))
comp1 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.3)
assert comp1.looks_like(a1, a2)
comp2 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.15)
assert not comp2.looks_like(a1, a2)
comp3 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.02,
pair_cor_max=0.7,
dE=0.3)
assert not comp3.looks_like(a1, a2)
hard_E_comp = EnergyComparator(dE=1.0)
assert hard_E_comp.looks_like(a1, a2)
soft_E_comp = EnergyComparator(dE=.01)
assert not soft_E_comp.looks_like(a1, a2)
set_raw_score(a1, .1)
set_raw_score(a2, .27)
rs_comp = RawScoreComparator(0.15)
assert not rs_comp.looks_like(a1, a2)
comp1 = SequentialComparator([hard_E_comp, rs_comp], [0, 0])
assert not comp1.looks_like(a1, a2)
comp2 = SequentialComparator([hard_E_comp, rs_comp], [0, 1])
assert comp2.looks_like(a1, a2)
ejp_struct.set_cell(cellpar)
else:
logging.critical("CANNOT GET EJP STRUCTURE")
continue
pcy_struct = pcy_result['structures'][-1]
args = np.argsort(ejp_struct.positions[:, 2])
ejp_struct = ejp_struct[args]
args = np.argsort(pcy_struct.positions[:, 2])
pcy_struct = pcy_struct[args]
if len(ejp_struct) != len(pcy_struct):
logging.critical("N_ATOMS: %s VS. %s" % (len(ejp_struct), len(pcy_struct)))
continue
ejp_symbs, pcy_symbs = set(ejp_struct.get_chemical_symbols()), set(pcy_struct.get_chemical_symbols())
if ejp_symbs != pcy_symbs:
logging.info("DIFFERENT SYMBOLS: %s VS. %s" % (ejp_symbs, pcy_symbs))
continue
ejp_struct.calc, pcy_struct.calc = Mock(), Mock() # code below does not work without this
if cmp_atoms.looks_like(ejp_struct, pcy_struct):
dd = distance(pcy_struct, ejp_struct)
if dd > 2:
logging.info("STRUCTURE DIFF IS VERY BIG: %s" % dd)
else:
logging.critical("STRUCTURES ARE DIFFERENT")
logging.info("Done in %1.2f sc" % (time.time() - starttime))
from ase.calculators.singlepoint import SinglePointCalculator
a1 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.5, 0, 0], [1.5, 1.5, 0]])
a2 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.4, 0, 0], [1.5, 1.5, 0]])
e1 = 1.0
e2 = 0.8
a1.set_calculator(SinglePointCalculator(e1, None, None, None, a1))
a2.set_calculator(SinglePointCalculator(e2, None, None, None, a2))
comp1 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.3)
assert comp1.looks_like(a1, a2)
comp2 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.15)
assert not comp2.looks_like(a1, a2)
comp3 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.02,
pair_cor_max=0.7,
dE=0.3)
assert not comp3.looks_like(a1, a2)
from ase.ga import set_raw_score
a1 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.5, 0, 0], [1.5, 1.5, 0]])
a2 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.4, 0, 0], [1.5, 1.5, 0]])
e1 = 1.0
e2 = 0.8
a1.set_calculator(SinglePointCalculator(a1, energy=e1))
a2.set_calculator(SinglePointCalculator(a2, energy=e2))
comp1 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.3)
assert comp1.looks_like(a1, a2)
comp2 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.03,
pair_cor_max=0.7,
dE=0.15)
assert not comp2.looks_like(a1, a2)
comp3 = InteratomicDistanceComparator(n_top=3,
pair_cor_cum_diff=0.02,
pair_cor_max=0.7,
dE=0.3)
assert not comp3.looks_like(a1, a2)
hard_E_comp = EnergyComparator(dE=1.0)
assert hard_E_comp.looks_like(a1, a2)