def generator(group):
structures = []
for position in ["ontop", "bridge"]:
slab = fcc111("Au", size=group["repeats"].value(), vacuum=10.0)
add_adsorbate(slab, "Au", 3, position=position)
slab = fixBelow(slab, slab.positions[:, 2].min() + 1e-2)
slab.set_calculator(EMT())
structures.append(slab)
return structures
def asesurf2xxyz(symb, lattice, index, size=(1,1,3), vac=15.0, orthogonal=0):
"""
An interface function for ase.lattice.surface
Usage:
>>> atoms = asesurf2xxyz(symb, lattice, index, size,
vac=15.0, orthogonal=0))
Parameters:
symb: atomic symbol
lattice: 'fcc', 'bcc', or 'hcp0001'
index: '100', '111' or '110' (if lattice is 'hcp0001', this will not work.)
size: the number of atoms per each vector
Optional Parameters:
vac (default: 15.0 angstron): the thickness of space normal to the surface
orthogonal (default: False) : if True, two lateral cell vectors will be
orthogonal.
Example:
>>> Fe_100_1x1 = asesurf2xxyz('Fe', 'bcc', '100', (1,1,2))
>>> Au_111_2x2 = asesurf2xxyz('Au', 'fcc', '111', (1,1,3))
"""
if lattice == 'fcc':
if index == '100': at_ase = AS.fcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.fcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.fcc110(symb, size, vacuum=vac)
else: raise ValueError, "100, 111, or 110 surface is supported."
elif lattice == 'bcc':
if index == '100': at_ase = AS.bcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.bcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.bcc110(symb, size,
orthogonal=orthogonal,
vacuum=vac)
else: raise ValueError, "100, 111, or 110 surface is supported."
elif lattice == 'hcp0001':
at_ase = AS.hcp0001(symb, size, orthogonal=orthogonal, vacuum=vac)
else: raise ValueError, "fcc, bcc, or hcp0001 surface is supported."
symbols = at_ase.get_chemical_symbols()
posits = at_ase.get_positions()
cell = at_ase.get_cell()
pbc = at_ase.get_pbc()
atoms = []; i=0
for sym in symbols:
temp_at = Atom(sym, list(posits[i]))
atoms.append(temp_at.copy()); i+=1
at_xxyz = AtomsSystem(atoms, cell=cell, pbc=pbc)
return at_xxyz
def asesurf2xxyz(symb, lattice, index, size=(1,1,3), vac=15.0, orthogonal=0):
"""
An interface function for ase.lattice.surface
Usage:
>>> atoms = asesurf2xxyz(symb, lattice, index, size,
vac=15.0, orthogonal=0))
Parameters:
symb: atomic symbol
lattice: 'fcc', 'bcc', or 'hcp0001'
index: '100', '111' or '110' (if lattice is 'hcp0001', this will not work.)
size: the number of atoms per each vector
Optional Parameters:
vac (default: 15.0 angstron): the thickness of space normal to the surface
orthogonal (default: False) : if True, two lateral cell vectors will be
orthogonal.
Example:
>>> Fe_100_1x1 = asesurf2xxyz('Fe', 'bcc', '100', (1,1,2))
>>> Au_111_2x2 = asesurf2xxyz('Au', 'fcc', '111', (1,1,3))
"""
if lattice == 'fcc':
if index == '100': at_ase = AS.fcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.fcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.fcc110(symb, size, vacuum=vac)
else: raise ValueError("100, 111, or 110 surface is supported.")
elif lattice == 'bcc':
if index == '100': at_ase = AS.bcc100(symb, size, vacuum=vac)
elif index == '111': at_ase = AS.bcc111(symb, size,
orthogonal=orthogonal,
vacuum=vac)
elif index == '110': at_ase = AS.bcc110(symb, size,
orthogonal=orthogonal,
vacuum=vac)
else: raise ValueError("100, 111, or 110 surface is supported.")
elif lattice == 'hcp0001':
at_ase = AS.hcp0001(symb, size, orthogonal=orthogonal, vacuum=vac)
else: raise ValueError("fcc, bcc, or hcp0001 surface is supported.")
symbols = at_ase.get_chemical_symbols()
posits = at_ase.get_positions()
cell = at_ase.get_cell()
pbc = at_ase.get_pbc()
atoms = []; i=0
for sym in symbols:
temp_at = Atom(sym, list(posits[i]))
atoms.append(temp_at.copy()); i+=1
at_xxyz = AtomsSystem(atoms, cell=cell, pbc=pbc)
return at_xxyz
def get_surface_slabs(symbol,
surfacetype,
surfacesize,
layers,
latticeconstants,
vacuum=10.0):
images = []
if surfacetype == 'fcc100' or surfacetype == 'fcc111':
nlayeratoms = surfacesize[0] * surfacesize[1]
if isinstance(latticeconstants, (list, tuple)):
if not len(latticeconstants) == 1:
raise ValueError("Too many latticeconstants")
a = latticeconstants[0]
else:
a = latticeconstants
elif surfacetype == 'hcp0001':
nlayeratoms = surfacesize[0] * surfacesize[1]
if isinstance(latticeconstants, (list, tuple)):
if not len(latticeconstants) == 2:
raise ValueError("Latticeconstants must be on the form [a, c]")
a = latticeconstants[0]
c = latticeconstants[1]
else:
raise ValueError("Latticeconstants must be on the form [a, c]")
else:
raise ValueError("Surface type '%s' is not supported" %
(surfacetype, ))
for n in layers:
size = surfacesize + (n, )
if surfacetype == 'fcc100':
images.append(fcc100(symbol=symbol, size=size, a=a, vacuum=vacuum))
elif surfacetype == 'fcc111':
images.append(
fcc111(symbol=symbol,
size=size,
a=a,
vacuum=vacuum,
orthogonal=True))
elif surfacetype == 'hcp0001':
images.append(
hcp0001(symbol=symbol,
size=size,
a=a,
c=c,
vacuum=vacuum,
orthogonal=True))
return images, nlayeratoms
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_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 main(argv=[]):
kwargs = getArgs(argv)
elm = kwargs['element']
a = kwargs['lattice_constant']
size = kwargs['size']
orth = kwargs['orthogonal']
vac = kwargs['vacuum'] / 2 # applies to both sides of the slab
fix = kwargs['fix']
pad = kwargs['pad']
slab = fcc111(elm, size=size, a=a, orthogonal=orth, vacuum=vac)
# adjust cell
minA = min([p[2] for p in slab.get_positions() if p[2] > 0])
slab.translate((0, 0, -1 * minA))
# set contraints
constraint = FixAtoms(mask=[a.tag < fix for a in slab])
slab.set_constraint(constraint)
# write POSCAR
write('POSCAR' + pad, slab, format='vasp', direct=True)
def get_surface_slabs(symbol, surfacetype, surfacesize, layers, latticeconstants,
vacuum=10.0):
images = []
if surfacetype == 'fcc100' or surfacetype == 'fcc111':
nlayeratoms = surfacesize[0] * surfacesize[1]
if isinstance(latticeconstants, (list, tuple)):
if not len(latticeconstants) == 1:
raise ValueError("Too many latticeconstants")
a = latticeconstants[0]
else:
a = latticeconstants
elif surfacetype == 'hcp0001':
nlayeratoms = surfacesize[0] * surfacesize[1]
if isinstance(latticeconstants, (list, tuple)):
if not len(latticeconstants) == 2:
raise ValueError("Latticeconstants must be on the form [a, c]")
a = latticeconstants[0]
c = latticeconstants[1]
else:
raise ValueError("Latticeconstants must be on the form [a, c]")
else:
raise ValueError("Surface type '%s' is not supported" % (surfacetype,))
for n in layers:
size = surfacesize + (n,)
if surfacetype == 'fcc100':
images.append(fcc100(symbol=symbol, size=size, a=a, vacuum=vacuum))
elif surfacetype == 'fcc111':
images.append(fcc111(symbol=symbol, size=size, a=a, vacuum=vacuum,
orthogonal=True))
elif surfacetype == 'hcp0001':
images.append(hcp0001(symbol=symbol, size=size, a=a, c=c,
vacuum=vacuum, orthogonal=True))
return images, nlayeratoms
from ase.lattice.surface import fcc111, hcp0001
from ase.lattice.hexagonal import *
from ase import io
from os import system
import math
POSCAR_string = "B N Al"
lattice_constant_Al = 4.050
a_lattice_constant_BN = 2.5040
c_lattice_constant_BN = 6.6612
slab = fcc111('Al',
size=(7, 7, 3),
a=lattice_constant_Al,
orthogonal=False,
vacuum=0.0)
bn = hcp0001('B',
size=(8, 8, 2),
a=a_lattice_constant_BN,
c=0.0000001,
vacuum=0.0)
cell = bn.get_cell()
#cell[2][2]=20.0
bn.translate([0, 0, 10])
num_each = bn.get_number_of_atoms() / 2
bn.set_atomic_numbers([5] * num_each + [7] * num_each)
bn.extend(slab)
from ase.calculators.emt import EMT
from ase.constraints import FixBondLengths
from ase.optimize import BFGS, QuasiNewton
from ase.neb import SingleCalculatorNEB
from ase.lattice.surface import fcc111, add_adsorbate
from math import sqrt, cos, sin
for mic in [ False, True ]:
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)
calc = EMT()
slab.set_calculator(calc)
if mic:
# Remap into the cell so bond is actually wrapped.
slab.set_scaled_positions(slab.get_scaled_positions()%1.0)
constraint = FixBondLengths([[-3,-2],[-3,-1]], mic=True, atoms=slab)
else:
constraint = FixBondLengths([[-3,-2],[-3,-1]])
slab.set_constraint(constraint)
#!/usr/bin/env python
from ase.calculators.aims import Aims
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase import Atoms, Atom
from ase.io import write
atoms = fcc111('Pt', size=(1, 1, 4), vacuum=5.0)
atoms.cell = atoms.cell*2.809/2.77185858
constraint = FixAtoms(mask=[atom.position[2] < (atoms.cell[2][2]/2.0 + 0.5)
for atom in atoms])
atoms.set_constraint(constraint)
write('images/pt-slab-114-relax.png', atoms, show_unit_cell=2)
calc = Aims(label='surfaces/pt-slab-114-relax',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
kpts=(3, 3, 1),
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-2,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-2,
relax_geometry = 'bfgs 1.e-3')
atoms.set_calculator(calc)
print('energy = {0} eV'.format(atoms.get_potential_energy()))
print('Forces')
print('=======')
print(atoms.get_forces())
for i in range(1, len(atoms)):
from ase import units
from ase.md import MDLogger
T = 100. # temperature
folder = 'data'
nk = 1
r0list = linspace(20,300,50)
fric = 0.002 # equilibration time tau = 10 fs/fric
mdsteps = 1000
d = 2.934
for R in r0list:
print 'radius',R
name=(folder,'%.1f' %R)
atoms = fcc111('Au',size=(2,2,1),a=sqrt(2)*d)
L = atoms.get_cell().diagonal()
atoms. set_cell(L)
angle = L[1]/R
atoms.rotate('y',pi/2)
atoms.translate( (-atoms[0].x,0,0) )
atoms.translate((R,0,0))
atoms = Atoms(atoms=atoms,container='Wedge')
atoms.set_container(angle=angle,height=L[0],physical=False,pbcz=True)
calc = Hotbit(SCC=False,txt='%s/optimization_%s.cal' %name,kpts=(nk,1,nk),physical_k=False)
atoms.set_calculator(calc)
traj = PickleTrajectory( 'md_R%.3f-T%.0f.traj' %(R,T),'w',atoms)
dyn = Langevin(atoms,dt*units.fs,units.kB*T,fric)
from ase import *
from math import asin, pi, sqrt
from gpaw import GPAW
from ase.lattice.surface import fcc111
# Define geometry of slab + BF4:
slab = fcc111('Au', size=(2, 2, 3),orthogonal=True)
slab.center(axis=2, vacuum=12)
d=0.8
tFB1 = Atoms([Atom('B', (0, 0, 0)),
Atom('F', (d, d, d)),
Atom('F', (-d, -d, d)),
Atom('F', (-d, d, -d)),
Atom('F', (d, -d, -d))])
tFB1.rotate('y',pi/4,center=(0, 0, 0))
tFB1.rotate('x',asin(1/sqrt(3))+pi,center=(0, 0, 0))
tFB1.rotate('z',pi/3,center=(0, 0, 0))
tFB1.translate(slab.positions[5]+(0.,0.,5.118))
slab += tFB1
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
#print mask
slab.set_constraint(constraints.FixAtoms(mask=mask))
# Initial state:
calc = GPAW(h=0.16, kpts=(4, 4, 1), txt='22.txt',parallel={'domain':4}, xc='RPBE')
slab.set_calculator(calc)
qn=optimize.QuasiNewton(slab,trajectory='22.traj',restart='22.pckl')
qn.run(fmax=0.05)
#!/usr/bin/env python
from ase.lattice.surface import fcc111
atoms = fcc111('Al', size=(2, 2, 4), vacuum=10.0)
print([atom.z for atom in atoms])
print [atom.z <= 13 for atom in atoms]
from ase.lattice.surface import fcc111
from ase.io import write
slab = fcc111('Al', size=(2, 2, 3), vacuum=10.0)
write('images/Al-slab.png', slab, rotation='90x', show_unit_cell=2)
from vasp import Vasp
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
atoms = fcc111("Pt", size=(2, 2, 3), vacuum=10.0)
# note this function only works when atoms are created by the surface module.
add_adsorbate(atoms, "O", height=1.2, position="hcp")
constraint = FixAtoms(mask=[atom.symbol != "O" for atom in atoms])
atoms.set_constraint(constraint)
from ase.io import write
write("images/Pt-hcp-o-site.png", atoms, show_unit_cell=2)
print(
Vasp("surfaces/Pt-slab-O-hcp", xc="PBE", kpts=[4, 4, 1], encut=350, ibrion=2, nsw=25, atoms=atoms).potential_energy
)
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.lattice.surface import fcc111, add_adsorbate
h = 1.85
d = 1.10
slab = fcc111('Cu', size=(4, 4, 2), vacuum=10.0)
slab.set_calculator(EMT())
e_slab = slab.get_potential_energy()
molecule = Atoms('2N', positions=[(0., 0., 0.), (0., 0., d)])
molecule.set_calculator(EMT())
e_N2 = molecule.get_potential_energy()
add_adsorbate(slab, molecule, h, 'ontop')
constraint = FixAtoms(mask=[a.symbol != 'N' for a in slab])
slab.set_constraint(constraint)
dyn = QuasiNewton(slab, trajectory='N2Cu.traj')
dyn.run(fmax=0.05)
print('Adsorption energy:', e_slab + e_N2 - slab.get_potential_energy())
from jasp import *
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase.io import write
atoms = fcc111('Pt', size=(1, 1, 3), vacuum=10.0)
# note this function only works when atoms are created by the surface module.
add_adsorbate(atoms, 'O', height=1.2, position='fcc')
constraint = FixAtoms(mask=[atom.symbol != 'O' for atom in atoms])
atoms.set_constraint(constraint)
write('images/Pt-o-fcc-1ML.png', atoms, show_unit_cell=2)
with jasp('surfaces/Pt-slab-1x1-O-fcc',
xc='PBE',
kpts=(8, 8, 1),
encut=350,
ibrion=2,
nsw=25,
atoms=atoms) as calc:
print atoms.get_potential_energy()
from ase import Atoms
from ase.lattice.surface import fcc111, add_adsorbate
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.io import write
# Find the initial and final states for the reaction.
# Set up a (4 x 4) two layer slab of Cu:
slab = fcc111('Cu',size=(4,4,2))
slab.set_pbc((1,1,0))
# Initial state.
# Add the N2 molecule oriented at 60 degrees:
d = 1.10 # N2 bond length
N2mol = Atoms('N2',positions=[[0.0,0.0,0.0],[0.5*3**0.5*d,0.5*d,0.0]])
add_adsorbate(slab,N2mol,height=1.0,position='fcc')
# Use the EMT calculator for the forces and energies:
slab.set_calculator(EMT())
# We don't want to worry about the Cu degrees of freedom,
# so fix these atoms:
mask = [atom.symbol == 'Cu' for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))
from ase import Atoms
from ase.visualize import view
from ase.calculators.vasp import Vasp
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.lattice.surface import fcc111, add_adsorbate
from ase.io import write
from ase.io.trajectory import PickleTrajectory
import io
import os
#Date: 4/17/15
#sets up the slab and molecule
slab = fcc111('Pd', size=(3, 3, 2), vacuum=10)
molecule = Atoms('CO', [(0., 0., 0.), (0., 0., 1.13)])
add_adsorbate(slab, molecule, 1.7, 'ontop')
#sets up the calculator
calc = EMT()
slab.set_calculator(calc)
#runs optimization
dyn = QuasiNewton(slab, trajectory='CO-Pd-ontop.traj')
dyn.run(fmax=0.05)
#writes the trajectory file in .xyz format
traj = PickleTrajectory("CO-Pd-ontop.traj")
nsteps = dyn.get_number_of_steps()
string = 'structure'
try:
from ase.calculators.d3ef import d3ef
except ImportError:
fortran = False
def testforce(system, fortran=False, bj=False):
system.set_calculator(D3(fortran=fortran, bj=bj))
f1 = system.get_forces()
f2 = numeric_forces(system, d=0.0001)
assert abs(f1 - f2).max() < 1e-6
waterdim = create_s22_system('Water_dimer')
slab = fcc111('Au', (1, 1, 4), vacuum=7.5)
testforce(waterdim, fortran=False, bj=False)
#testforce(slab, fortran=False, bj=False) # This is too slow!
testforce(waterdim, fortran=False, bj=True)
#testforce(slab, fortran=False, bj=True) # This is too slow!
if fortran:
testforce(waterdim, fortran=True, bj=False)
testforce(slab, fortran=True, bj=False)
testforce(waterdim, fortran=True, bj=True)
testforce(slab, fortran=True, bj=True)
import numpy
from ase import io
from ase import Atoms
from ase.visualize import view
from ase.lattice.surface import fcc111
#lattice_constant = 4.01 # http://www.hindawi.com/journals/apc/2011/305634/ GGA-PBE
lattice_constant = 3.975 # vasp, Pt@PBE
# experiment is 3.92
#lattice_constant = 4.1839615096998237
#lattice_constant = 4.06 # this is what I get for the 18e psp from Paratec
slab = fcc111('Pt',
size=(4, 4, 9),
a=lattice_constant,
vacuum=0.0,
orthogonal=True)
print 'used ', lattice_constant
io.write('slab.vasp', slab)
print 'Warning, Z-component of poscar seems to be incorrect'
io.write('slab.xyz', slab)
x1 = 4 * (lattice_constant * (1. / 2)**.5)
x2 = 4 * (lattice_constant * (1. / 2)**.5) * numpy.cos(60 * numpy.pi / 180)
y2 = 4 * (lattice_constant * (1. / 2)**.5) * numpy.sin(60 * numpy.pi / 180)
print 'Angstrom '
print str(round(x1, 6)), 0.00, 0.00
print str(round(x2, 6)), str(round(y2, 6)), 0.00
from jasp import *
from ase.lattice.surface import fcc111
atoms = fcc111('Pt', size=(2, 2, 4), vacuum=10.0, a=3.986)
atoms.append(Atom('C', [atoms[12].x, atoms[12].y, atoms[12].z + 1.851]))
atoms.append(Atom('O', [atoms[-1].x, atoms[-1].y, atoms[-1].z + 1.157]))
for field in [-0.5, 0.0, 0.5]:
with jasp('surfaces/Pt-co-field-{0}'.format(field),
xc='PBE',
encut=350,
kpts=(6,6,1),
efield=field, # set the field
ldipol=True, # turn dipole correction on
idipol=3, # set field in z-direction
atoms=atoms) as calc:
try:
print '{0}: {1:1.3f}'.format(field, atoms.get_potential_energy())
except (VaspSubmitted, VaspQueued):
pass
from ase.constraints import FixAtoms
def check_forces():
"""Makes sure the unconstrained forces stay that way."""
forces = atoms.get_forces(apply_constraint=False)
funconstrained = float(forces[0, 0])
forces = atoms.get_forces(apply_constraint=True)
forces = atoms.get_forces(apply_constraint=False)
funconstrained2 = float(forces[0, 0])
assert funconstrained2 == funconstrained
atoms = fcc111('Cu', (2, 2, 1), vacuum=10.)
atoms[0].x += 0.2
atoms.set_constraint(FixAtoms(indices=[atom.index for atom in atoms]))
# First run the tes with EMT and save a force component.
atoms.set_calculator(EMT())
check_forces()
f = float(atoms.get_forces(apply_constraint=False)[0, 0])
# Save and reload with a SinglePointCalculator.
atoms.write('singlepointtest.traj')
atoms = read('singlepointtest.traj')
check_forces()
# Manually change a value.
forces = atoms.get_forces(apply_constraint=False)
import numpy as np
from ase import Atoms, Atom
from ase.lattice.surface import fcc111, fcc211, add_adsorbate
atoms = fcc211('Au', (3, 5, 8), vacuum=10.)
assert len(atoms) == 120
atoms = atoms.repeat((2, 1, 1))
assert np.allclose(atoms.get_distance(0, 130), 2.88499566724)
atoms = fcc111('Ni', (2, 2, 4), orthogonal=True)
add_adsorbate(atoms, 'H', 1, 'bridge')
add_adsorbate(atoms, Atom('O'), 1, 'fcc')
add_adsorbate(atoms, Atoms('F'), 1, 'hcp')
# The next test ensures that a simple string of multiple atoms cannot be used,
# which should fail with a KeyError that reports the name of the molecule due
# to the string failing to work with Atom().
failed = False
try:
add_adsorbate(atoms, 'CN', 1, 'ontop')
except KeyError as e:
failed = True
assert e.args[0] == 'CN'
assert failed
from ase.lattice.surface import fcc111
atoms = fcc111('Al', size=(2, 2, 4), vacuum=10.0)
print([atom.z for atom in atoms])
print[atom.z <= 13 for atom in atoms]
from gpaw import GPAW
from ase.lattice.surface import fcc111
from ase.lattice.surface import add_adsorbate
atoms = fcc111('Pt', (2, 2, 6), a=4.00, vacuum=10.0)
add_adsorbate(atoms, 'O', 2.0, 'fcc')
calc = GPAW(mode='pw',
kpts=(8, 8, 1),
xc='RPBE')
ncpus = 4
#!/usr/bin/env python
from ase.calculators.aims import Aims
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase import Atoms, Atom
from ase.io import write
adsorbate = Atoms('CO')
adsorbate[1].z = 1.13
atoms = fcc111('Pt', size=(1, 1, 3), vacuum=10.0)
# note this function only works when atoms are created by the surface module.
add_adsorbate(atoms, adsorbate, height=1.2, position='fcc')
constraint = FixAtoms(mask=[atom.symbol != 'O' and atom.symbol != 'C'
for atom in atoms])
atoms.set_constraint(constraint)
write('images/pt-fcc-site.png', atoms, show_unit_cell=2)
calc = Aims(label='surfaces/pt-slab-co-fcc',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
kpts=(3, 3, 1),
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-2,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-2,
relax_geometry = 'bfgs 1.e-2')
atoms.set_calculator(calc)
print('energy = {0} eV'.format(atoms.get_potential_energy()))
print(atoms.get_forces())
# This test verifies that energy and forces are (approximately)
# parallelization independent
#
# Tests the LCAO energy and forces in non-orthogonal cell with
# simultaneous parallelization over bands, domains and k-points (if
# enough CPUs are available), both with and without scalapack
# (if scalapack is available).
#
# Run with 1, 2, 4 or 8 (best) CPUs.
#
# This test covers many cases not caught by lcao_parallel or
# lcao_parallel_kpt
#
# Written November 24, 2011, r8567
system = fcc111('Au', size=(1, 3, 1))
system.numbers[0] = 8
# It is important that the number of atoms is uneven; this
# tests the case where the band parallelization does not match
# the partitioning of orbitals between atoms (the middle atom has orbitals
# on distinct band descriptor ranks)
system.center(vacuum=3.5, axis=2)
system.rattle(stdev=0.2, seed=17)
#from ase.visualize import view
#view(system)
#system.set_pbc(0)
#system.center(vacuum=3.5)
from gpaw import FermiDirac
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase import Atoms, Atom
from ase.io import write
from ase.visualize import view
def sortz(atoms):
tags = atoms.positions[:,2]
deco = sorted([(tag, i) for i, tag in enumerate(tags)])
indices = [i for tag, i in deco]
return atoms[indices]
adsorbate = molecule('CO')
adsorbate2 = molecule('O2')
atoms = fcc111('Pt', size=(4, 4, 2), vacuum=6.0)
# note this function only works when atoms are created by the surface module.
add_adsorbate(atoms, adsorbate, height=3.0, position='ontop')
add_adsorbate(atoms, adsorbate2, height=3.0, position='fcc')
atoms = sortz(atoms)
atoms.translate([0, 0, -atoms[0].z])
mask=[atom.index for atom in atoms if atom.symbol == 'O' or atom.symbol == 'C']
mol = atoms[mask]
del atoms[mask]
mol.cell[0:2, ] = mol.cell[0:2, ]*1/3.0
mol.cell[2][2] = 3
mol[-1].z = mol[-3].z
mol[-1].position = mol[-1].position + mol.cell[0]/6 + mol.cell[1]/6
mol.translate([0, 0, -mol[1].z])
mol = mol*[3, 3, 2]
# compute local potential of slab with no dipole
from ase.lattice.surface import fcc111, add_adsorbate
from jasp import *
import matplotlib.pyplot as plt
from ase.io import write
slab = fcc111('Al', size=(2, 2, 2), vacuum=10.0)
add_adsorbate(slab, 'Na', height=1.2, position='fcc')
slab.center()
write('images/Na-Al-slab.png', slab, rotation='-90x', show_unit_cell=2)
with jasp('surfaces/Al-Na-nodip',
xc='PBE',
encut=340,
kpts=(2, 2, 1),
lvtot=True, # write out local potential
lvhar=True, # write out only electrostatic potential, not xc pot
atoms=slab) as calc:
calc.calculate()
from ase import *
from math import asin, pi, sqrt
from gpaw import GPAW
from ase.lattice.surface import fcc111
# Define geometry of slab + BF4:
slab = fcc111('Au', size=(6, 4, 3),orthogonal=True)
slab.center(axis=2, vacuum=12)
d=0.8
tFB1 = Atoms([Atom('B', (0, 0, 0)),
Atom('F', (d, d, d)),
Atom('F', (-d, -d, d)),
Atom('F', (-d, d, -d)),
Atom('F', (d, -d, -d))])
tFB1.rotate('y',pi/4,center=(0, 0, 0))
tFB1.rotate('x',asin(1/sqrt(3))+pi,center=(0, 0, 0))
tFB1.rotate('z',pi/3,center=(0, 0, 0))
tFB1.translate(slab.positions[25]+(0.,0.,5.118))
slab += tFB1
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
#print mask
slab.set_constraint(constraints.FixAtoms(mask=mask))
calc = GPAW(h=0.16, kpts=(2, 3, 1), txt='64.txt',parallel={'domain':64}, xc='RPBE')
slab.set_calculator(calc)
qn=optimize.QuasiNewton(slab,trajectory='64.traj',restart='64.pckl')
qn.run(fmax=0.05)
qn.attach(calc.write,1,'64.gpw')
from ase.ga.data import PrepareDB
from ase.ga.startgenerator import StartGenerator
from ase.ga.utilities import closest_distances_generator
from ase.ga.utilities import get_all_atom_types
from ase.constraints import FixAtoms
import numpy as np
from ase.lattice.surface import fcc111
db_file = 'gadb.db'
# create the surface
slab = fcc111('Au', size=(4, 4, 1), vacuum=10.0, orthogonal=True)
slab.set_constraint(FixAtoms(mask=len(slab) * [True]))
# define the volume in which the adsorbed cluster is optimized
# the volume is defined by a corner position (p0)
# and three spanning vectors (v1, v2, v3)
pos = slab.get_positions()
cell = slab.get_cell()
p0 = np.array([0., 0., max(pos[:, 2]) + 2.])
v1 = cell[0, :] * 0.8
v2 = cell[1, :] * 0.8
v3 = cell[2, :]
v3[2] = 3.
# Define the composition of the atoms to optimize
atom_numbers = 2 * [47] + 2 * [79]
# define the closest distance two atoms of a given species can be to each other
unique_atom_types = get_all_atom_types(slab, atom_numbers)
cd = closest_distances_generator(atom_numbers=unique_atom_types,
from ase.lattice.surface import fcc111
from vasp import Vasp
slab = fcc111('Al', size=(1, 1, 4), vacuum=10.0)
calc = Vasp('surfaces/Al-bandstructure',
xc='PBE',
encut=300,
kpts=[6, 6, 6],
lcharg=True, # you need the charge density
lwave=True, # and wavecar for the restart
atoms=slab)
n, bands, p = calc.get_bandstructure(kpts_path=[(r'$\Gamma$', [0, 0, 0]),
('$K1$', [0.5, 0.0, 0.0]),
('$K1$', [0.5, 0.0, 0.0]),
('$K2$', [0.5, 0.5, 0.0]),
('$K2$', [0.5, 0.5, 0.0]),
(r'$\Gamma$', [0, 0, 0]),
(r'$\Gamma$', [0, 0, 0]),
('$K3$', [0.0, 0.0, 1.0])],
kpts_nintersections=10)
p.savefig('images/Al-slab-bandstructure.png')
from vasp import Vasp
from ase.lattice.surface import fcc111
import matplotlib.pyplot as plt
Nlayers = [3, 4, 5, 6, 7, 8, 9, 10, 11]
energies = []
sigmas = []
for n in Nlayers:
slab = fcc111('Cu', size=(1, 1, n), vacuum=10.0)
slab.center()
calc = Vasp('bulk/Cu-layers/{0}'.format(n),
xc='PBE',
encut=350,
kpts=[8, 8, 1],
atoms=slab)
calc.set_nbands(f=2) # the default nbands in VASP is too low for Cu
energies.append(slab.get_potential_energy())
calc.stop_if(None in energies)
for i in range(len(Nlayers) - 1):
N = Nlayers[i]
DeltaE_N = energies[i + 1] - energies[i]
sigma = 0.5 * (-N * energies[i + 1] + (N + 1) * energies[i])
sigmas.append(sigma)
print 'nlayers = {1:2d} sigma = {0:1.3f} eV/atom'.format(sigma, N)
plt.plot(Nlayers[0:-1], sigmas, 'bo-')
plt.xlabel('Number of layers')
plt.ylabel('Surface energy (eV/atom)')
plt.savefig('images/Cu-unrelaxed-surface-energy.png')
from ase.io import read
from ase.lattice.surface import fcc111, add_adsorbate, fcc100, fcc110, hcp0001, bcc111
import os
import sys
import shutil
nargs = len(sys.argv)
argv1 = sys.argv[1]
argv2 = sys.argv[2]
fname = 'scratch/structure' + argv1
tmpDir = os.getenv('PBSTMPDIR')
folder = 'scratch/vasp' + argv1
#lattice and initial atom setup for unit cell
slab = fcc111('Pt', size=(3, 3, 3), vacuum=10)
add_adsorbate(slab, 'Au', 2.5, 'fcc')
#current position read in
slabatoms = read(fname)
slab.set_positions(slabatoms.get_positions())
mask = [atom.tag > 2 for atom in slab]
slab.set_constraint(FixAtoms(mask=mask))
calc = Vasp(xc='PBE',
lreal='Auto',
kpts=[2, 2, 1],
ismear=1,
sigma=0.2,
algo='fast',
istart=0,
'bands': -2}, txt='CO_lumo.txt')
calc = GPAW(nbands=60, h=0.2, xc='RPBE', kpts=(8,6,1),
eigensolver='cg',
spinpol=True,
mixer=MixerSum(nmaxold=5, beta=0.1, weight=100),
convergence={'energy': 100,
'density': 100,
'eigenstates': 1.0e-7,
'bands': -10}, txt=filename+'.txt')
#----------------------------------------
# Import Slab with relaxed CO
#slab = Calculator('gs.gpw').get_atoms()
slab = fcc111('Pt', size=(1, 2, 3), orthogonal=True)
add_adsorbate(slab, 'C', 2.0, 'ontop')
add_adsorbate(slab, 'O', 3.15, 'ontop')
slab.center(axis=2, vacuum=4.0)
view(slab)
molecule = slab.copy()
del molecule [:-2]
# Molecule
#----------------
molecule.set_calculator(c_mol)
molecule.get_potential_energy()
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.lattice.surface 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.structure 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))
#!/usr/bin/env python
from jasp import *
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
atoms = fcc111('Pt', size=(2, 2, 3), vacuum=10.0)
# note this function only works when atoms are created by the surface module.
add_adsorbate(atoms, 'O', height=1.2, position='hcp')
constraint = FixAtoms(mask=[atom.symbol != 'O' for atom in atoms])
atoms.set_constraint(constraint)
from ase.io import write
write('images/Pt-hcp-o-site.png', atoms, show_unit_cell=2)
with jasp('surfaces/Pt-slab-O-hcp',
xc='PBE',
kpts=(4, 4, 1),
encut=350,
ibrion=2,
nsw=25,
atoms=atoms) as calc:
calc.calculate()
#!/usr/bin/env python
from ase.lattice.surface import fcc111
import ase
import kmcos
import kmcos
from kmcos.utils import get_ase_constructor
from kmcos.types import *
import numpy as np
slab = fcc111('Pt', [1,1,4], vacuum=10)
positions = slab.get_scaled_positions()
model_name = str(__file__[+0:-3]).replace("__build", "") # This line automatically names the model based on the python file’s name. The brackets cut off zero characters from the beginning and three character from the end (".py"). The replace command removes the ‘__build’ part of the string. If you want to override this automatic naming, just set the variable ‘model_name’ equal to the string that you would like to use.
kmc_model = kmcos.create_kmc_model(model_name)
kmc_model.set_meta(model_name='pt111',
model_dimension='2',
author='Max J. Hoffmann',
email='*****@*****.**',
debug=0)
layer = Layer(name='pt111')
pos1 = np.array([positions[1, 0],
positions[1, 1], 0.672])
layer.add_site(Site(name='hollow1',
pos=pos1))
pos2 = np.array([positions[2, 0],
positions[2, 1], 0.672])
import numpy as np
from ase import Atoms, Atom
from ase.lattice.surface import fcc111, fcc211, add_adsorbate
atoms = fcc211("Au", (3, 5, 8), vacuum=10.0)
assert len(atoms) == 120
atoms = atoms.repeat((2, 1, 1))
assert np.allclose(atoms.get_distance(0, 130), 2.88499566724)
atoms = fcc111("Ni", (2, 2, 4), orthogonal=True)
add_adsorbate(atoms, "H", 1, "bridge")
add_adsorbate(atoms, Atom("O"), 1, "fcc")
add_adsorbate(atoms, Atoms("F"), 1, "hcp")
# The next test ensures that a simple string of multiple atoms cannot be used,
# which should fail with a KeyError that reports the name of the molecule due
# to the string failing to work with Atom().
failed = False
try:
add_adsorbate(atoms, "CN", 1, "ontop")
except KeyError as e:
failed = True
assert e.args[0] == "CN"
assert failed
from ase.ga.startgenerator import StartGenerator
from ase.ga.utilities import closest_distances_generator, atoms_too_close
from ase.ga.cutandsplicepairing import CutAndSplicePairing
import numpy as np
from ase.lattice.surface import fcc111
from ase.constraints import FixAtoms
# first create two random starting candidates
slab = fcc111("Au", size=(4, 4, 2), vacuum=10.0, orthogonal=True)
slab.set_constraint(FixAtoms(mask=slab.positions[:, 2] <= 10.0))
pos = slab.get_positions()
cell = slab.get_cell()
p0 = np.array([0.0, 0.0, max(pos[:, 2]) + 2.0])
v1 = cell[0, :] * 0.8
v2 = cell[1, :] * 0.8
v3 = cell[2, :]
v3[2] = 3.0
cd = closest_distances_generator(atom_numbers=[47, 79], ratio_of_covalent_radii=0.7)
atom_numbers = 2 * [47] + 2 * [79]
sg = StartGenerator(
slab=slab, atom_numbers=atom_numbers, closest_allowed_distances=cd, box_to_place_in=[p0, [v1, v2, v3]]
)
c1 = sg.get_new_candidate()
c1.info["confid"] = 1
c2 = sg.get_new_candidate()
c2.info["confid"] = 2
# Benzene on the slab
from jasp import *
from ase.lattice.surface import fcc111, add_adsorbate
from ase.structure import molecule
from ase.constraints import FixAtoms
atoms = fcc111('Au', size=(3,3,3), vacuum=10)
benzene = molecule('C6H6')
benzene.translate(-benzene.get_center_of_mass())
# I want the benzene centered on the position in the middle of atoms
# 20, 22, 23 and 25
p = (atoms.positions[20] +
atoms.positions[22] +
atoms.positions[23] +
atoms.positions[25])/4.0 + [0.0, 0.0, 3.05]
benzene.translate(p)
atoms += benzene
# now we constrain the slab
c = FixAtoms(mask=[atom.symbol=='Au' for atom in atoms])
atoms.set_constraint(c)
#from ase.visualize import view; view(atoms)
with jasp('surfaces/Au-benzene-pbe',
xc='PBE',
encut=350,
kpts=(4,4,1),
ibrion=1,
nsw=100,
atoms=atoms) as calc:
print atoms.get_potential_energy()
from ase import io
from ase import Atoms
from ase.visualize import view
from ase.lattice.surface import fcc111
vasp_GW_project = 4.1839615096998237 # this is the lattice const I used for most MD
vasp_Au_vdWDF = 4.25
vasp_Au_ariel = 4.16089
experiment = 4.08
lattice_const = vasp_GW_project
slab = fcc111('Au',
size=(5, 5, 6),
a=lattice_const,
vacuum=0.0,
orthogonal=False)
view(slab)
print('used ', lattice_const)
io.write('slab.cube', slab)
io.write('slab.xyz', slab)
x1 = 5 * (lattice_const * (1. / 2)**.5)
x2 = 5 * (lattice_const * (1. / 2)**.5) * numpy.cos(60 * numpy.pi / 180)
y2 = 5 * (lattice_const * (1. / 2)**.5) * numpy.sin(60 * numpy.pi / 180)
print('Angstrom ')
print(str(round(x1, 6)), 0.00, 0.00)
print(str(round(x2, 6)), str(round(y2, 6)), 0.00)