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import numpy as np
import pytest
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.calculators.fd import (
calculate_numerical_forces,
calculate_numerical_stress,
)
from ase.data.s22 import create_s22_system
releps = 1e-6
abseps = 1e-8
pytestmark = [pytest.mark.calculator('dftd3'),
pytest.mark.calculator_lite]
def close(val, reference, releps=releps, abseps=abseps):
print(val, reference)
assert np.abs(val - reference) < max(np.abs(releps * reference), abseps)
def array_close(val, reference, releps=releps, abseps=abseps):
valflat = val.flatten()
refflat = reference.flatten()
for i, vali in enumerate(valflat):
close(vali, refflat[i], releps, abseps)
@pytest.fixture()
def system():
return create_s22_system('Adenine-thymine_complex_stack')
def test_forces(factory, system):
# do all non-periodic calculations with Adenine-Thymine complex
# Default is D3(zero)
system.calc = factory.calc()
close(system.get_potential_energy(), -0.6681154466652238)
# Only check forces once, for the default settings.
f_ref = np.array(
[[0.0088385621657399, -0.0118387210205813, -0.0143242057174889],
[-0.0346912282737323, 0.0177797757792533, -0.0442349785529711],
[0.0022759961575945, -0.0087458217241648, -0.0051887171699909],
[-0.0049317224619103, -0.0215152368018880, -0.0062290998430756],
[-0.0013032612752381, -0.0356240144088481, 0.0203401124180720],
[-0.0110305568118348, -0.0182773178473497, -0.0023730575217145],
[0.0036258610447203, -0.0074994162928053, -0.0144058177906650],
[0.0005289754841564, -0.0035901842246731, -0.0103580836569947],
[0.0051775352510856, -0.0051076755874038, -0.0103428268442285],
[0.0011299493448658, -0.0185829345539878, -0.0087205807334006],
[0.0128459160503721, -0.0248356605575975, 0.0007946691695359],
[-0.0063194401470256, -0.0058117310787239, -0.0067932156139914],
[0.0013749100498893, -0.0118259631230572, -0.0235404547526578],
[0.0219558160992901, -0.0087512938555865, -0.0226017156485839],
[0.0001168268736984, -0.0138384169778581, -0.0014850073023105],
[0.0037893625607261, 0.0117649062330659, 0.0162375798918204],
[0.0011352730068862, 0.0142002748861793, 0.0129337874676760],
[-0.0049945288501837, 0.0073929058490670, 0.0088391871214417],
[0.0039715118075548, 0.0186949615105239, 0.0114822052853407],
[-0.0008003587963147, 0.0161735976004718, 0.0050357997715004],
[-0.0033142342134453, 0.0153658921418049, -0.0026233088963388],
[-0.0025451124688653, 0.0067994927521733, -0.0017127589489137],
[-0.0010451311609669, 0.0067173068779992, 0.0044413725566098],
[-0.0030829302438095, 0.0112138539867057, 0.0151213034444885],
[0.0117240581287903, 0.0161749855643631, 0.0173269837053235],
[-0.0025949288306356, 0.0158830629834040, 0.0155589787340858],
[0.0083784268665834, 0.0082132824775010, 0.0090603749323848],
[-0.0019694065480327, 0.0115576523485515, 0.0083901101633852],
[-0.0020036820791533, 0.0109276020920431, 0.0204922407855956],
[-0.0062424587308054, 0.0069848349714167, 0.0088791235460659]])
array_close(system.get_forces(), f_ref)
# calculate numerical forces, but use very loose comparison criteria!
# dftd3 doesn't print enough digits to stdout to get good convergence
f_numer = calculate_numerical_forces(system, eps=1e-4)
array_close(f_numer, f_ref, releps=1e-2, abseps=1e-3)
def test_d2_old(factory, system):
system.calc = factory.calc(old=True)
close(system.get_potential_energy(), -0.8923443424663762)
def test_d3_bj(factory, system):
system.calc = factory.calc(damping='bj')
close(system.get_potential_energy(), -1.211193213979179)
def test_d3_zerom(factory, system):
system.calc = factory.calc(damping='zerom')
close(system.get_potential_energy(), -2.4574447613705717)
def test_d3_bjm(factory, system):
system.calc = factory.calc(damping='bjm')
close(system.get_potential_energy(), -1.4662085277005799)
def test_alternative_tz(factory, system):
system.calc = factory.calc(tz=True)
close(system.get_potential_energy(), -0.6160295884482619)
def test_d3_zero_abc(factory, system):
system.calc = factory.calc(abc=True)
close(system.get_potential_energy(), -0.6528640090262864)
def test_d3_zero_revpbe(factory, system):
system.calc = factory.calc(xc='revpbe')
close(system.get_potential_energy(), -1.5274869363442936)
def test_bad_xc(factory, system):
system.calc = factory.calc(xc='does_not_exist')
with pytest.raises(RuntimeError, match='Unknown DFTD3 functional name'):
system.get_potential_energy()
def test_custom_damping(factory, system):
system.calc = factory.calc(s6=1.1, sr6=1.1, s8=0.6, sr8=0.9, alpha6=13.0)
close(system.get_potential_energy(), -1.082846357973487)
def test_d3_bj_abc(factory, system):
# A couple of combinations, but not comprehensive
system.calc = factory.calc(damping='bj', abc=True)
close(system.get_potential_energy(), -1.1959417763402416)
def test_d3_zerom_b3lyp(factory, system):
system.calc = factory.calc(damping='zerom', xc='b3-lyp')
close(system.get_potential_energy(), -1.3369234231047677)
def test_diamond_stress(factory, system):
system = bulk('C')
system.calc = factory.calc()
close(system.get_potential_energy(), -0.2160072476277501)
# Do one stress for the default settings
s_ref = np.array([0.0182329043326,
0.0182329043326,
0.0182329043326,
-3.22757439831e-14,
-3.22766949320e-14,
-3.22766949320e-14])
array_close(system.get_stress(), s_ref)
# As with numerical forces, numerical stresses will not be very well
# converged due to the limited number of digits printed to stdout
# by dftd3. So, use very loose comparison criteria.
s_numer = calculate_numerical_stress(system, eps=1e-4)
array_close(s_numer, s_ref, releps=1e-2, abseps=1e-3)
def test_free_energy_bug(factory):
# Energy and free_energy should be close to equal.
# Due to a bug related to legacy free_energy property handling,
# it would double-count the free energy from the DFT calculation.
# This test protects against that.
atoms = bulk('Au', cubic=True)
atoms.rattle(stdev=0.15)
dftd3 = factory.calc(dft=EMT())
atoms.calc = dftd3
e1, e2 = (atoms.get_potential_energy(force_consistent=x)
for x in [False, True])
assert e1 == pytest.approx(e2, abs=1e-14)
class EMTWithMagmoms(EMT):
implemented_properties = [*EMT.implemented_properties, 'magmoms']
def dummy_magmoms(self, atoms):
return 1.234 + np.arange(len(atoms))
def calculate(self, atoms, *args, **kwargs):
super().calculate(atoms, *args, **kwargs)
self.results['magmoms'] = self.dummy_magmoms(atoms)
def test_non_dftd3_property(factory):
dft = EMTWithMagmoms()
calc = factory.calc(dft=dft)
# Our DFTD3 calculator should advertise that it supports this property:
assert 'magmoms' in calc.implemented_properties
atoms = bulk('Au', cubic=True)
atoms.calc = calc
magmoms = atoms.get_magnetic_moments()
assert magmoms == pytest.approx(dft.dummy_magmoms(atoms))
print('magmoms', magmoms)
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