def cssm(metal, data_dict): # cleave_stable_surfaces_from_metals
name = 'POSCAR_' + metal
if metal in bcc: # For bcc metals, cleave 110 surface
lattice_a = float(data_dict.get(metal)[2])
for i in range(1, 4):
name_out = name + '_' + str(i)
slab = bcc110(metal, a=lattice_a, size=(i, i, 4), vacuum=7.5)
'''(i,i,4) means repeat i i 4 in x y and z directions. vacuum will be 7.5 * 2 because it was added on the two sides.'''
constraint_l = FixAtoms(indices=[
atom.index for atom in slab if atom.index < i * i * 2
])
slab.set_constraint(constraint_l)
ase.io.write(name_out, slab, format='vasp')
### Add the element line to the POSCAR file ###
subprocess.call(['sed -i ' + '\'5a' + metal + '\' ' + name_out],
shell=True)
bottom(name_out)
elif metal in hcp: # For hcp metals, cleave 0001 surface
lattice_a, lattice_c = [float(i) for i in data_dict.get(metal)[2:]]
for i in range(1, 4):
name_out = name + '_' + str(i)
slab = hcp0001(metal,
a=lattice_a,
c=lattice_c,
size=(i, i, 4),
vacuum=7.5)
constraint_l = FixAtoms(indices=[
atom.index for atom in slab if atom.index < i * i * 2
])
slab.set_constraint(constraint_l)
ase.io.write(name_out, slab, format='vasp')
subprocess.call(['sed -i ' + '\'5a' + metal + '\' ' + name_out],
shell=True)
bottom(name_out)
elif metal in fcc: # For fcc metals, cleave 111 surface
lattice_a = float(data_dict.get(metal)[2])
for i in range(1, 4):
name_out = name + '_' + str(i)
slab = fcc111(metal, a=lattice_a, size=(i, i, 4), vacuum=7.5)
# slab.center(vacuum=7.5, axis = 2)
constraint_l = FixAtoms(indices=[
atom.index for atom in slab if atom.index < i * i * 2
])
slab.set_constraint(constraint_l)
ase.io.write(name_out, slab, format='vasp')
subprocess.call(['sed -i ' + '\'5a' + metal + '\' ' + name_out],
shell=True)
bottom(name_out)
else:
print(
'Please add your element in the crystal structure lists: bcc, hcp, and fcc'
)
def hcp0001_root(symbol, root, size, a=None, c=None,
vacuum=None, orthogonal=False):
"""HCP(0001) surface maniupulated to have a x unit side length
of *root* before repeating. This also results in *root* number
of repetitions of the cell.
The first 20 valid roots for nonorthogonal are...
1, 3, 4, 7, 9, 12, 13, 16, 19, 21, 25,
27, 28, 31, 36, 37, 39, 43, 48, 49"""
atoms = hcp0001(symbol=symbol, size=(1, 1, size[2]),
a=a, c=c, vacuum=vacuum, orthogonal=orthogonal)
atoms = root_surface(atoms, root)
atoms *= (size[0], size[1], 1)
return atoms
def test_root_surf():
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)
# Right number of atoms
assert len(atoms1) == len(atoms2) == 14
# Same positions
assert (atoms1.positions == atoms2.positions).all()
# Same cell
assert (atoms1.cell == atoms2.cell).all()
def hcp0001_root(symbol,
root,
size,
a=None,
c=None,
vacuum=None,
orthogonal=False):
"""HCP(0001) surface maniupulated to have a x unit side length
of *root* before repeating.This also results in *root* number
of repetitions of the cell.
The first 20 valid roots for nonorthogonal are...
1, 3, 4, 7, 9, 12, 13, 16, 19, 21, 25,
27, 28, 31, 36, 37, 39, 43, 48, 49"""
atoms = hcp0001(symbol=symbol,
size=(1, 1, size[2]),
a=a,
c=c,
vacuum=vacuum,
orthogonal=orthogonal)
atoms = root_surface(atoms, root)
atoms *= (size[0], size[1], 1)
return atoms
# Vacuum and hcp lattice parameter for graphene
d = 4.0
a = 2.4437
calc = GPAW(h=0.15,
xc='LDA',
nbands=-4,
txt='-',
basis='dzp',
convergence={
'energy': 1e-5,
'density': 1e-5
})
# Calculate potential energy per atom for orthogonal unitcell
atoms = hcp0001('C', a=a / sqrt(3), vacuum=d, size=(3, 2, 1), orthogonal=True)
del atoms[[1, -1]]
atoms.center(axis=0)
atoms.set_calculator(calc)
kpts_c = np.ceil(50 / np.sum(atoms.get_cell()**2, axis=1)**0.5).astype(int)
kpts_c[~atoms.get_pbc()] = 1
calc.set(kpts=kpts_c)
eppa1 = atoms.get_potential_energy() / len(atoms)
F1_av = atoms.get_forces()
equal(np.abs(F1_av).max(), 0, 5e-3)
# Redo calculation with non-orthogonal unitcell
atoms = Atoms(symbols='C2',
pbc=(True, True, False),
positions=[(a / 2, -sqrt(3) / 6 * a, d),
from ase.io import Trajectory
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0, b, b), (b, 0, b), (b, b, 0)], pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
def opt_hcp0001(self, c: int = None) -> None:
''' Optimize hcp0001 slab '''
slab = hcp0001(self.symbol, self.repeats_surface, self.a, c,
self.vacuum)
self.prepare_slab_opt(slab)
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
b = a / 2
cu = Atoms('Cu',
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1) * (6, 6, 6)
cu.set_calculator(EMT())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = LBFGS(f)
t = Trajectory('Cu-fcc.traj', 'w', cu)
opt.attach(t)
opt.run(5.0)
# HCP:
from ase.build import hcp0001
cu = hcp0001('Cu', (1, 1, 2), a=a / sqrt(2))
cu.cell[1, 0] += 0.05
cu *= (6, 6, 3)
cu.set_calculator(EMT())
print(cu.get_forces())
print(cu.get_stress())
f = UnitCellFilter(cu)
opt = MDMin(f, dt=0.01)
t = Trajectory('Cu-hcp.traj', 'w', cu)
opt.attach(t)
opt.run(0.2)
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)
from __future__ import print_function
import numpy as np
from ase.dft.kpoints import monkhorst_pack
from ase.parallel import paropen
from ase.build import hcp0001, add_adsorbate
from gpaw import GPAW, PW, FermiDirac, MixerSum
from gpaw.xc.exx import EXX
kpts = monkhorst_pack((16, 16, 1))
kpts += np.array([1 / 32., 1 / 32., 0])
a = 2.51 # Lattice parameter of Co
slab = hcp0001('Co', a=a, c=4.07, size=(1, 1, 4))
pos = slab.get_positions()
cell = slab.get_cell()
cell[2, 2] = 20. + pos[-1, 2]
slab.set_cell(cell)
slab.set_initial_magnetic_moments([0.7, 0.7, 0.7, 0.7])
ds = [1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.5, 3.75, 4.0, 5.0, 6.0, 10.0]
for d in ds:
pos = slab.get_positions()
add_adsorbate(slab, 'C', d, position=(pos[3, 0], pos[3, 1]))
add_adsorbate(slab,
'C',
d,
position=(cell[0, 0] / 3 + cell[1, 0] / 3,
cell[0, 1] / 3 + cell[1, 1] / 3))
#view(slab)
calc = GPAW(xc='PBE',
def create_bimetal_surf(composition,
surf_type,
size,
latt='',
fix_layers=2,
vacuum=12.0):
"""
Create bimetallic surfaces
composition: "M1" - single-metal
"M1,M2,config" - bimetallic surface with the configuration
latt:
"""
# extract lattice constants if available
if latt == '':
if composition == 'Co' and surf_type == 'fcc111':
a_latt = 3.544
else:
a_latt, c_latt = (None, None)
else:
tmp = latt.split(',')
a_latt = float(tmp[0])
if len(tmp) > 1:
c_latt = float(tmp[1])
# set the surface type name
if surf_type == 'fcc111':
surf_type_name = '111'
elif surf_type == 'hcp0001':
surf_type_name = '0001'
# set the metallic surface slab
tmp = composition.split(',')
M1_name = tmp[0]
if len(tmp) > 1:
M2_name = tmp[1]
config = tmp[2]
else:
M2_name = ''
config = ''
if not "bulk" in config:
if surf_type == 'fcc111':
surf = fcc111(M1_name, a=a_latt, size=size, vacuum=vacuum)
elif surf_type == 'hcp0001':
surf = hcp0001(M1_name,
a=a_latt,
c=c_latt,
size=size,
vacuum=vacuum)
surf_name = M1_name + surf_type_name + "-%d%d%d" % (size[0], size[1],
size[2])
if M2_name != '':
surf_name = surf_name + '-' + config_bimetal + "-" + M2_name
if config_bimetal == 'top':
for atom in surf:
if atom.tag == 1:
atom.symbol = M2_name
elif config_bimetal == 'sub':
for atom in surf:
if atom.tag == 2:
atom.symbol = M2_name
elif config_bimetal == 'mixtop':
for atom in surf:
if atom.tag == 1:
atom.symbol = M2_name
break
elif config_bimetal == 'mixsub':
for atom in surf:
if atom.tag == 2:
atom.symbol = M2_name
break
else:
print "ERROR: Not implemented yet for the bimetal configuration %s!!!" % (
config)
# get the number of layers
nlayers = max(surf.get_tags())
mask = [atom.tag > nlayers - fix_layers for atom in surf]
constr_bottom = FixAtoms(mask=mask)
surf.set_constraint([constr_bottom])
return surf, surf_name
def build():
p = OptionParser(usage='%prog [options] [ads@]surf [output file]',
version='%prog 0.1',
description='Example ads/surf: fcc-CO@2x2Ru0001')
p.add_option('-l', '--layers', type='int',
default=4,
help='Number of layers.')
p.add_option('-v', '--vacuum', type='float',
default=5.0,
help='Vacuum.')
p.add_option('-x', '--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'hcp'])
p.add_option('-a', '--lattice-constant', type='float',
help='Lattice constant in Angstrom.')
p.add_option('--c-over-a', type='float',
help='c/a ratio.')
p.add_option('--height', type='float',
help='Height of adsorbate over surface.')
p.add_option('--distance', type='float',
help='Distance between adsorbate and nearest surface atoms.')
p.add_option('-M', '--magnetic-moment', type='float', default=0.0,
help='Magnetic moment.')
p.add_option('-G', '--gui', action='store_true',
help="Pop up ASE's GUI.")
p.add_option('-P', '--python', action='store_true',
help="Write Python script.")
opt, args = p.parse_args()
if not 1 <= len(args) <= 2:
p.error("incorrect number of arguments")
if '@' in args[0]:
ads, surf = args[0].split('@')
else:
ads = None
surf = args[0]
if surf[0].isdigit():
i1 = surf.index('x')
n = int(surf[:i1])
i2 = i1 + 1
while surf[i2].isdigit():
i2 += 1
m = int(surf[i1 + 1:i2])
surf = surf[i2:]
else:
n = 1
m = 1
if surf[-1].isdigit():
if surf[1].isdigit():
face = surf[1:]
surf = surf[0]
else:
face = surf[2:]
surf = surf[:2]
else:
face = None
Z = atomic_numbers[surf]
state = reference_states[Z]
if opt.crystal_structure:
x = opt.crystal_structure
else:
x = state['symmetry']
if opt.lattice_constant:
a = opt.lattice_constant
else:
a = estimate_lattice_constant(surf, x, opt.c_over_a)
script = ['from ase.build import ',
'vac = %r' % opt.vacuum,
'a = %r' % a]
if x == 'fcc':
if face is None:
face = '111'
slab = fcc111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'fcc111'
script += ['slab = fcc111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)]
r = a / np.sqrt(2) / 2
elif x == 'bcc':
if face is None:
face = '110'
if face == '110':
slab = bcc110(surf, (n, m, opt.layers), a, opt.vacuum)
elif face == '100':
slab = bcc100(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'bcc' + face
script += ['slab = bcc%s(%r, (%d, %d, %d), a, vac)' %
(face, surf, n, m, opt.layers)]
r = a * np.sqrt(3) / 4
elif x == 'hcp':
if face is None:
face = '0001'
if opt.c_over_a is None:
c = np.sqrt(8 / 3.0) * a
else:
c = opt.c_over_a * a
slab = hcp0001(surf, (n, m, opt.layers), a, c, opt.vacuum)
script[0] += 'hcp0001'
script += ['c = %r * a' % (c / a),
'slab = hcp0001(%r, (%d, %d, %d), a, c, vac)' %
(surf, n, m, opt.layers)]
r = a / 2
elif x == 'diamond':
if face is None:
face = '111'
slab = diamond111(surf, (n, m, opt.layers), a, opt.vacuum)
script[0] += 'diamond111'
script += ['slab = diamond111(%r, (%d, %d, %d), a, vac)' %
(surf, n, m, opt.layers)]
r = a * np.sqrt(3) / 8
else:
raise NotImplementedError
magmom = opt.magnetic_moment
if magmom is None:
magmom = {'Ni': 0.6, 'Co': 1.2, 'Fe': 2.3}.get(surf, 0.0)
slab.set_initial_magnetic_moments([magmom] * len(slab))
if magmom != 0:
script += ['slab.set_initial_magnetic_moments([%r] * len(slab))' %
magmom]
slab.pbc = 1
script += ['slab.pbc = True']
name = '%dx%d%s%s' % (n, m, surf, face)
if ads:
site = 'ontop'
if '-' in ads:
site, ads = ads.split('-')
name = site + '-' + ads + '@' + name
symbols = string2symbols(ads)
nads = len(symbols)
if nads == 1:
script[:0] = ['from ase import Atoms']
script += ['ads = Atoms(%r)' % ads]
ads = Atoms(ads)
else:
script[:0] = ['from ase.build import molecule']
script += ['ads = molecule(%r)' % ads]
ads = molecule(ads)
add_adsorbate(slab, ads, 0.0, site)
d = opt.distance
if d is None:
d = r + covalent_radii[ads[0].number] / 2
h = opt.height
if h is None:
R = slab.positions
y = ((R[:-nads] - R[-nads])**2).sum(1).min()**0.5
h = (d**2 - y**2)**0.5
else:
assert opt.distance is None
slab.positions[-nads:, 2] += h
script[1] += ', add_adsorbate'
script += ['add_adsorbate(slab, ads, %r, %r)' % (h, site)]
if len(args) == 2:
write(args[1], slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % args[1]]
elif not opt.gui:
write(name + '.traj', slab)
script[1:1] = ['from ase.io import write']
script += ['write(%r, slab)' % (name + '.traj')]
if opt.gui:
view(slab)
script[1:1] = ['from ase.visualize import view']
script += ['view(slab)']
if opt.python:
print('\n'.join(script))
def adsorb(db, height=1.2, nlayers=3, nkpts=7, ecut=400):
"""Adsorb nitrogen in hcp-site on Ru(0001) surface.
Do calculations for N/Ru(0001), Ru(0001) and a nitrogen atom
if they have not already been done.
db: Database
Database for collecting results.
height: float
Height of N-atom above top Ru-layer.
nlayers: int
Number of Ru-layers.
nkpts: int
Use a (nkpts * nkpts) Monkhorst-Pack grid that includes the
Gamma point.
ecut: float
Cutoff energy for plane waves.
Returns height.
"""
name = f'Ru{nlayers}-{nkpts}x{nkpts}-{ecut:.0f}'
parameters = dict(mode=PW(ecut),
eigensolver=Davidson(niter=2),
poissonsolver={'dipolelayer': 'xy'},
kpts={'size': (nkpts, nkpts, 1), 'gamma': True},
xc='PBE')
# N/Ru(0001):
slab = hcp0001('Ru', a=a, c=c, size=(1, 1, nlayers))
z = slab.positions[:, 2].max() + height
x, y = np.dot([2 / 3, 2 / 3], slab.cell[:2, :2])
slab.append('N')
slab.positions[-1] = [x, y, z]
slab.center(vacuum=vacuum, axis=2) # 2: z-axis
# Fix first nlayer atoms:
slab.constraints = FixAtoms(indices=list(range(nlayers)))
id = db.reserve(name=f'N/{nlayers}Ru(0001)', nkpts=nkpts, ecut=ecut)
if id is not None: # skip calculation if already done
slab.calc = GPAW(txt='N' + name + '.txt',
**parameters)
optimizer = BFGSLineSearch(slab, logfile='N' + name + '.opt')
optimizer.run(fmax=0.01)
height = slab.positions[-1, 2] - slab.positions[:-1, 2].max()
del db[id]
db.write(slab,
name=f'N/{nlayers}Ru(0001)', nkpts=nkpts, ecut=ecut,
height=height)
# Clean surface (single point calculation):
id = db.reserve(name=f'{nlayers}Ru(0001)', nkpts=nkpts, ecut=ecut)
if id is not None:
del slab[-1] # remove nitrogen atom
slab.calc = GPAW(txt=name + '.txt',
**parameters)
slab.get_forces()
del db[id]
db.write(slab,
name=f'{nlayers}Ru(0001)', nkpts=nkpts, ecut=ecut)
# Nitrogen atom:
id = db.reserve(name='N-atom', ecut=ecut)
if id is not None:
# Create spin-polarized nitrogen atom:
molecule = Atoms('N', magmoms=[3])
molecule.center(vacuum=4.0)
# Remove parameters that make no sense for an isolated atom:
del parameters['kpts']
del parameters['poissonsolver']
# Calculate energy:
molecule.calc = GPAW(txt=name + '.txt', **parameters)
molecule.get_potential_energy()
del db[id]
db.write(molecule, name='N-atom', ecut=ecut)
return height
from sys import argv
from ase.build import hcp0001, add_adsorbate
from ase.constraints import FixAtoms
from ase.optimize.lbfgs import LBFGS
from gpaw import GPAW, Mixer, FermiDirac
tag = 'Ru001_Ru8'
adsorbate_heights = {'H': 1.0, 'N': 1.108, 'O': 1.257}
slab = hcp0001('Ru',
size=(2, 2, 4),
a=2.72,
c=1.58 * 2.72,
vacuum=7.0,
orthogonal=True)
slab.center(axis=2)
if len(argv) > 1:
adsorbate = argv[1]
tag = adsorbate + tag
add_adsorbate(slab, adsorbate, adsorbate_heights[adsorbate], 'hcp')
slab.set_constraint(FixAtoms(mask=slab.get_tags() >= 3))
calc = GPAW(xc='PBE',
h=0.2,
mixer=Mixer(0.1, 5, weight=100.0),
occupations=FermiDirac(width=0.1),
kpts=[4, 4, 1],
setups={'Ru': '8'},
from ase.build import fcc111
from ase.build import bcc111
from ase.build import hcp0001
from ase.build import fcc111_root
from ase.build import root_surface
from ase.build import root_surface_analysis
# Make samples of primitive cell
prim_fcc111 = fcc111("H", (1, 1, 2), a=1)
prim_bcc111 = bcc111("H", (1, 1, 2), a=1)
prim_hcp0001 = hcp0001("H", (1, 1, 2), a=1)
# Check valid roots up to root 21 (the 10th root cell)
valid_fcc111 = root_surface_analysis(prim_fcc111, 21)
valid_bcc111 = root_surface_analysis(prim_bcc111, 21)
valid_hcp0001 = root_surface_analysis(prim_hcp0001, 21)
# These should have different positions, but the same
# cell geometry.
assert valid_fcc111 == valid_bcc111 == valid_hcp0001
# Make an easy sample to check code errors
atoms1 = root_surface(prim_fcc111, 7)
# Ensure the valid roots are the roots are valid against
# a set of manually checked roots for this system
assert valid_fcc111 == [1.0, 3.0, 4.0, 7.0, 9.0,
12.0, 13.0, 16.0, 19.0, 21.0]
# Remake easy sample using surface function
atoms2 = fcc111_root("H", 7, (1, 1, 2), a=1)
