def test_au111(wrap):
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.set_calculator(calc)
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%d.traj' % wrap)
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
assert abs(slab.get_distance(-2, -1, mic=1) - d2) < 1e-9
def test_qmmm_acn():
import numpy as np
import ase.units as units
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec,
sigma_me, sigma_c, sigma_n,
epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, LJInteractionsGeneral, EIQMMM
from ase.constraints import FixLinearTriatomic
from ase.optimize import BFGS
# From https://www.sciencedirect.com/science/article/pii/S0166128099002079
eref = 4.9 * units.kcal / units.mol
dref = 3.368
aref = 79.1
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
inter = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN(), vacuum=3.0),
EIQMMM([0, 1, 2], ACN(), ACN(), inter),
EIQMMM([0, 1, 2], ACN(), ACN(), inter, vacuum=3.0),
EIQMMM([3, 4, 5], ACN(), ACN(), inter, vacuum=3.0)]:
dimer = Atoms('CCNCCN',
[(-r_mec, 0, 0),
(0, 0, 0),
(r_cn, 0, 0),
(r_mec, 3.7, 0),
(0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
dimer.calc = calc
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
opt = BFGS(dimer, maxstep=0.04,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.001, steps=1000)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(1, 4)
a0 = dimer.get_angle(2, 1, 4)
fmt = '{0:>25}: {1:.3f} {2:.3f} {3:.1f}'
print(fmt.format(calc.name, -e0, d0, a0))
assert abs(e0 + eref) < 0.013
assert abs(d0 - dref) < 0.224
assert abs(a0 - aref) < 2.9
print(fmt.format('reference', eref, dref, aref))
def test_rattle_linear():
"""Test RATTLE and QM/MM for rigid linear acetonitrile."""
import numpy as np
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec, sigma_me, sigma_c,
sigma_n, epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractionsGeneral
from ase.md.verlet import VelocityVerlet
from ase.constraints import FixLinearTriatomic
import ase.units as units
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [
ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
EIQMMM([0, 1, 2], ACN(), ACN(), i)
]:
dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0),
(r_mec, 3.7, 0), (0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
dimer.calc = calc
d1 = dimer[:3].get_all_distances()
d2 = dimer[3:].get_all_distances()
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
2.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=20)
md.run(100)
de = dimer.get_potential_energy() - e
assert np.all(abs(dimer[:3].get_all_distances() - d1) < 1e-10)
assert np.all(abs(dimer[3:].get_all_distances() - d2) < 1e-10)
assert abs(de - -0.005) < 0.001
def test_CO2linear_Au111_langevin(testdir):
"""Test Langevin with constraints for rigid linear
triatomic molecules"""
rng = np.random.RandomState(0)
eref = 3.133526
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.calc = calc
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
fr = 0.1
dyn = Langevin(slab,
2.0 * units.fs,
temperature_K=300,
friction=fr,
trajectory='langevin_%.1f.traj' % fr,
logfile='langevin_%.1f.log' % fr,
loginterval=20,
rng=rng)
dyn.run(100)
# Check that the temperature is within a reasonable range
T = slab.get_temperature()
assert T > 100
assert T < 500
# Check that the constraints work
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
assert abs(slab.get_distance(-2, -1, mic=1) - d2) < 1e-9
# If the energy differs from the reference energy
# it is most probable that the redistribution of
# random forces in Langevin is not working properly
assert abs(slab.get_potential_energy() - eref) < 1e-4
def test_getindices():
from ase.build import fcc111
from ase.constraints import (FixAtoms, FixBondLengths, FixLinearTriatomic,
FixInternals, Hookean, constrained_indices)
slab = fcc111('Pt', (4, 4, 4))
C1 = FixAtoms([0, 2, 4])
C2 = FixBondLengths([[0, 1], [0, 2]])
C3 = FixInternals(bonds=[[1, [7, 8]], [1, [8, 9]]])
C4 = Hookean(a1=30, a2=40, rt=1.79, k=5.)
C5 = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
slab.set_constraint([C1, C2, C3, C4, C5])
assert all(
constrained_indices(slab, (FixAtoms, FixBondLengths)) == [0, 1, 2, 4])
assert all(
constrained_indices(slab, (FixBondLengths,
FixLinearTriatomic)) == [0, 1, 2, 3, 4, 5])
assert all(
constrained_indices(slab) == [0, 1, 2, 3, 4, 5, 7, 8, 9, 30, 40])
masses = atoms.get_masses()
masses[::3] = m_me
atoms.set_masses(masses)
# Determine side length of a box with the density of acetonitrile at 298 K
d = 0.776 / 1e24 # Density in g/Ang3 (https://pubs.acs.org/doi/10.1021/je00001a006)
L = ((masses.sum() / units.mol) / d)**(1 / 3.)
# Set up box of 27 acetonitrile molecules
atoms.set_cell((L, L, L))
atoms.center()
atoms = atoms.repeat((3, 3, 3))
atoms.set_pbc(True)
# Set constraints for rigid triatomic molecules
nm = 27
atoms.constraints = FixLinearTriatomic(triples=[(3 * i, 3 * i + 1, 3 * i + 2)
for i in range(nm)])
tag = 'acn_27mol_300K'
atoms.calc = ACN(rc=np.min(np.diag(atoms.cell)) / 2)
# Create Langevin object
md = Langevin(atoms,
1 * units.fs,
temperature=300 * units.kB,
friction=0.01,
logfile=tag + '.log')
traj = Trajectory(tag + '.traj', 'w', atoms)
md.attach(traj.write, interval=1)
md.run(5000)
i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [
ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
EIQMMM([0, 1, 2], ACN(), ACN(), i)
]:
dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0),
(r_mec, 3.7, 0), (0, 3.7, 0), (-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
dimer.calc = calc
d1 = dimer[:3].get_all_distances()
d2 = dimer[3:].get_all_distances()
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
2.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=20)
md.run(100)
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.set_calculator(calc)
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
fr = 0.1
dyn = Langevin(slab,
2.0 * units.fs,
300 * units.kB,
fr,
trajectory='langevin_%.1f.traj' % fr,
logfile='langevin_%.1f.log' % fr,
loginterval=20,
rng=rng)
dyn.run(100)
# Check that the temperature is within a reasonable range
T = slab.get_temperature()