atoms = Atoms([
Atom('Pd', [5.078689759346383, 5.410678028467162, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 4.000000000000000, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 6.821356056934325, 4.000000000000000]),
Atom('Pd', [6.707600438297196, 5.410678028467162, 6.303627574066606]),
Atom('N', [4.807604264052752, 5.728625577716107, 5.919407072553396]),
Atom('H', [4.000000000000000, 5.965167390141987, 6.490469524180266]),
])
constraint = FixAtoms(mask=[a.symbol == 'Pd' for a in atoms])
atoms.set_constraint(constraint)
atoms.center(vacuum=4.0)
atoms.set_pbc(False)
return atoms
def get_calculator():
calc = GPAW(gpts=(64, 64, 64), #h=0.18, gives 64x60x60
mode='lcao',
basis='szp(dzp)',
nbands=-5,
xc='LDA',
width=0.1,
mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0),
poissonsolver=PoissonSolver(nn='M', relax='GS'),
convergence={'energy': 1e-4, 'bands': -3},
stencils=(3, 3),
txt='nanoparticle.txt')
return calc
run_test(get_atoms, get_calculator, name, fmax=0.05, steps=200)
name = 'CO_Au111'
def get_atoms():
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
no2 = Atoms('CO',
positions=[(-xpos + 1.2, 0, -zpos),
(-xpos + 1.2, -1.1, -zpos)])
# Surface slab
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, no2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
#constraints
constraint = FixAtoms(mask=[(a.tag == 4) or (a.tag == 3) or (a.tag == 2)
for a in slab])
slab.set_constraint(constraint)
return slab
def get_calculator():
calc = EMT()
return calc
run_test(get_atoms, get_calculator, name, steps=200)
i = 0
for image in neb.images[1:-1]:
if not mpi.parallel or mpi.rank // (mpi.size // 3) == i:
image.set_calculator(calc)
i += 1
neb.set_calculator = set_calculator
return neb
def get_calculator_emt():
return EMT()
def get_calculator_gpaw():
if mpi.parallel:
assert mpi.size % 3 == 0
s = mpi.size // 3
r0 = mpi.rank // s * s
comm = range(r0, r0 + s)
else:
comm = mpi.world
calc = GPAW(h=0.25,
kpts=(2, 2, 1),
communicator=comm,
txt='neb-%d.txt' % r0)
return calc
run_test(get_atoms, get_calculator_emt, name + '-emt')
run_test(get_atoms, get_calculator_gpaw, name + '-gpaw')
from math import sin, cos, pi
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize.test import run_test
from ase.build import fcc111, add_adsorbate
name = 'CO_Au111'
def get_atoms():
zpos = cos(134.3/2.0*pi/180.0)*1.197
xpos = sin(134.3/2.0*pi/180.0)*1.19
no2 =Atoms('CO', positions=[(-xpos+1.2,0,-zpos), (-xpos+1.2,-1.1,-zpos)])
# Surface slab
slab =fcc111('Au', size=(2, 2, 4),vacuum=2*5, orthogonal = True )
slab.center()
add_adsorbate(slab,no2,1.5,'bridge')
slab.set_pbc((True,True,False))
#constraints
constraint = FixAtoms(mask=[(a.tag == 4) or (a.tag == 3) or (a.tag==2) for a in slab])
slab.set_constraint(constraint)
return slab
def get_calculator():
calc = EMT()
return calc
run_test(get_atoms, get_calculator, name, steps=200)
if not mpi.parallel or mpi.rank // (mpi.size // 3) == i:
image.set_calculator(calc)
i += 1
neb.set_calculator = set_calculator
return neb
def get_calculator_emt():
return EMT()
def get_calculator_gpaw():
if mpi.parallel:
assert mpi.size % 3 == 0
s = mpi.size // 3
r0 = mpi.rank // s * s
comm = range(r0, r0 + s)
else:
comm = mpi.world
calc = GPAW(h=0.25,
kpts=(2, 2, 1),
communicator=comm,
txt='neb-%d.txt' % r0)
return calc
run_test(get_atoms, get_calculator_emt, name + '-emt')
run_test(get_atoms, get_calculator_gpaw, name + '-gpaw')
(0.0582, 0.0582, 9.4227),
(2.5965, -0.2051, 9.4199),
(5.1282, 0.0663, 9.4037),
(7.6808, -0.0157, 9.4235),
(-0.2051, 2.5965, 9.4199),
(2.1913, 2.1913, 9.6123),
(5.0046, 2.5955, 9.4873),
(7.5409, 2.5336, 9.4126),
(0.0663, 5.1282, 9.4037),
(2.5955, 5.0046, 9.4873),
(5.3381, 5.3381, 9.6106),
(7.8015, 5.0682, 9.4237),
(-0.0157, 7.6808, 9.4235),
(2.5336, 7.5409, 9.4126),
(5.0682, 7.8015, 9.4237),
(7.6155, 7.6155, 9.4317)])
c2=Atoms('C2', [(3.2897, 3.2897, 10.6627),
(4.2113, 4.2113, 10.6493)])
srf.extend(c2)
srf.pbc=(1, 1, 0)
srf.set_cell([ 10.2106, 10.2106, 20.6572],scale_atoms=False)
mask=[a.index < 32 for a in srf]
c1 = FixedPlane(-1, (1/np.sqrt(2), 1/np.sqrt(2), 1))
c2 = FixedPlane(-2, (1/np.sqrt(2), 1/np.sqrt(2), 1))
constraint = FixAtoms(mask=mask)
srf.set_constraint([constraint, c1, c2])
return srf
run_test(get_atoms, get_calculator, 'C2_Cu100')
Atom('Cu', [ 8.433333333333335, 5.009870513769302, -2.146500000000000]),
Atom('Cu', [ 9.771531840491031, 4.244150023558828, -0.202086055768371]),
Atom('Cu', [ 11.133333333333335, 5.009870513769302, -2.146500000000000]),
Atom('Cu', [ 3.021531840490714, 6.582418613776583, -0.202086055768197]),
Atom('Cu', [ 4.383333333333334, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 5.721531840490814, 6.582418613776629, -0.202086055768203]),
Atom('Cu', [ 7.083333333333333, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 8.421531840490985, 6.582418613776876, -0.202086055768357]),
Atom('Cu', [ 9.783333333333335, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 11.121531840490929, 6.582418613776676, -0.202086055768221]),
Atom('Cu', [ 12.483333333333334, 7.348139103987287, -2.146500000000000]),
])
mask = [a.position[2] < -1 for a in slab]
slab.set_constraint(FixAtoms(mask=mask))
h = 1.85
d = 1.10
molecule = Atoms('2N', positions=[(0., 0., h),
(0., 0., h + d)])
molecule.set_calculator(EMT())
slab.extend(molecule)
return slab
def get_calculator():
return EMT()
run_test(get_atoms_surf, get_calculator, name + '-surf', steps=200)
run_test(get_atoms_adsorbate, get_calculator, name + '-N2', steps=200)
Atom('Cu', [ 11.133333333333335, 5.009870513769302, -2.146500000000000]),
Atom('Cu', [ 3.021531840490714, 6.582418613776583, -0.202086055768197]),
Atom('Cu', [ 4.383333333333334, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 5.721531840490814, 6.582418613776629, -0.202086055768203]),
Atom('Cu', [ 7.083333333333333, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 8.421531840490985, 6.582418613776876, -0.202086055768357]),
Atom('Cu', [ 9.783333333333335, 7.348139103987287, -2.146500000000000]),
Atom('Cu', [ 11.121531840490929, 6.582418613776676, -0.202086055768221]),
Atom('Cu', [ 12.483333333333334, 7.348139103987287, -2.146500000000000]),
])
mask = [a.position[2] < -1 for a in slab]
slab.set_constraint(FixAtoms(mask=mask))
a = 2.70
c = 1.59 * a
h = 1.85
d = 1.10
x = slab.positions[0, 2] / (c / 2) * 100
molecule = Atoms('2N', positions=[(0., 0., h),
(0., 0., h + d)])
molecule.set_calculator(EMT())
slab.extend(molecule)
return slab
def get_calculator():
return EMT()
run_test(get_atoms_surf, get_calculator, name + '-surf', steps=200)
run_test(get_atoms_adsorbate, get_calculator, name + '-N2', steps=200)
[5.00000011, 6.30002353, 5.9163716],
[5.88571848, 5.0122839, 6.82246859],
[5.88625613, 5.01308931, 5.01214155],
[7.14329342, 7.18115393, 6.81640316],
[7.14551332, 7.17200869, 5.00879027],
[8.41609966, 5.00661165, 5.02355167],
[8.41971183, 5.0251482, 6.83462168],
[9.69568096, 7.18645894, 6.8078633],
[9.68914668, 7.16663649, 5.00000011],
[10.95518898, 5.02163182, 6.8289018],
[11.83752486, 6.29836826, 5.90274952],
[10.94464142, 5.00000011, 5.01802495],
],
)
return atoms
def get_calculator():
calc = GPAW(
h=0.2,
mode="lcao",
basis="szp(dzp)",
mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0),
poissonsolver=PoissonSolver(nn="M", relax="GS"),
txt="C5H12.txt",
)
return calc
run_test(get_atoms, get_calculator, name + "-gpaw")
from ase.calculators.emt import EMT
from ase.lattice.cubic import FaceCenteredCubic
from ase.optimize.test import run_test
name = 'Cu_bulk'
def get_atoms():
atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,0], [0,0,1]],
size=(3,3,3), symbol='Cu', pbc=(1,1,1))
atoms.rattle(stdev=0.1,seed=42)
return atoms
def get_calculator():
return EMT()
run_test(get_atoms, get_calculator, name, fmax=0.02)
(1.2409, 1.2409, 7.6081), (3.7731, 1.2803, 7.6603),
(6.3219, 1.3241, 7.6442), (8.8935, 1.2669, 7.6189),
(1.2803, 3.7731, 7.6603), (3.8188, 3.8188, 7.5870),
(6.3457, 3.8718, 7.6649), (8.9174, 3.8340, 7.5976),
(1.3241, 6.3219, 7.6442), (3.8718, 6.3457, 7.6649),
(6.3945, 6.3945, 7.6495), (8.9576, 6.3976, 7.6213),
(1.2669, 8.8935, 7.6189), (3.8340, 8.9174, 7.5976),
(6.3976, 8.9576, 7.6213), (8.9367, 8.9367, 7.6539),
(0.0582, 0.0582, 9.4227), (2.5965, -0.2051, 9.4199),
(5.1282, 0.0663, 9.4037), (7.6808, -0.0157, 9.4235),
(-0.2051, 2.5965, 9.4199), (2.1913, 2.1913, 9.6123),
(5.0046, 2.5955, 9.4873), (7.5409, 2.5336, 9.4126),
(0.0663, 5.1282, 9.4037), (2.5955, 5.0046, 9.4873),
(5.3381, 5.3381, 9.6106), (7.8015, 5.0682, 9.4237),
(-0.0157, 7.6808, 9.4235), (2.5336, 7.5409, 9.4126),
(5.0682, 7.8015, 9.4237), (7.6155, 7.6155, 9.4317)])
c2 = Atoms('C2', [(3.2897, 3.2897, 10.6627), (4.2113, 4.2113, 10.6493)])
srf.extend(c2)
srf.pbc = (1, 1, 0)
srf.set_cell([10.2106, 10.2106, 20.6572], scale_atoms=False)
mask = [a.index < 32 for a in srf]
c1 = FixedPlane(-1, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
c2 = FixedPlane(-2, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
constraint = FixAtoms(mask=mask)
srf.set_constraint([constraint, c1, c2])
return srf
run_test(get_atoms, get_calculator, 'C2_Cu100')
[ 5.90380523, 5.65545388, 5.91569796],
[ 7.15617518, 6.52907738, 5.91569796],
[ 8.41815022, 5.66384716, 5.92196554],
[ 9.68108996, 6.52891016, 5.91022362],
[ 10.93006206, 5.65545388, 5.91569796],
[ 5.00000011, 6.30002353, 5.9163716 ],
[ 5.88571848, 5.0122839 , 6.82246859],
[ 5.88625613, 5.01308931, 5.01214155],
[ 7.14329342, 7.18115393, 6.81640316],
[ 7.14551332, 7.17200869, 5.00879027],
[ 8.41609966, 5.00661165, 5.02355167],
[ 8.41971183, 5.0251482 , 6.83462168],
[ 9.69568096, 7.18645894, 6.8078633 ],
[ 9.68914668, 7.16663649, 5.00000011],
[ 10.95518898, 5.02163182, 6.8289018 ],
[ 11.83752486, 6.29836826, 5.90274952],
[ 10.94464142, 5.00000011, 5.01802495]
])
return atoms
def get_calculator():
calc = GPAW(h=0.2,
mode = 'lcao',
basis = 'szp(dzp)',
mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0),
poissonsolver=PoissonSolver(nn='M', relax='GS'),
txt='C5H12.txt')
return calc
run_test(get_atoms, get_calculator, name + '-gpaw')