def get_atoms_surf():
a = 2.70
c = 1.59 * a
h = 1.85
d = 1.10
slab = Atoms('2Cu', [(0., 0., 0.), (1 / 3., 1 / 3., -0.5 * c)],
tags=(0, 1),
pbc=(1, 1, 0))
slab.set_cell([(a, 0, 0), (a / 2, 3**0.5 * a / 2, 0), (0, 0, 1)])
slab = slab.repeat((4, 4, 1))
mask = [a.tag == 1 for a in slab]
slab.set_constraint(FixAtoms(mask=mask))
return slab
def get_atoms():
srf = Atoms('Cu64', [(1.2763, 1.2763, 4.0000), (3.8290, 1.2763, 4.0000),
(6.3816, 1.2763, 4.0000), (8.9343, 1.2763, 4.0000),
(1.2763, 3.8290, 4.0000), (3.8290, 3.8290, 4.0000),
(6.3816, 3.8290, 4.0000), (8.9343, 3.8290, 4.0000),
(1.2763, 6.3816, 4.0000), (3.8290, 6.3816, 4.0000),
(6.3816, 6.3816, 4.0000), (8.9343, 6.3816, 4.0000),
(1.2763, 8.9343, 4.0000), (3.8290, 8.9343, 4.0000),
(6.3816, 8.9343, 4.0000), (8.9343, 8.9343, 4.0000),
(0.0000, 0.0000, 5.8050), (2.5527, 0.0000, 5.8050),
(5.1053, 0.0000, 5.8050), (7.6580, 0.0000, 5.8050),
(0.0000, 2.5527, 5.8050), (2.5527, 2.5527, 5.8050),
(5.1053, 2.5527, 5.8050), (7.6580, 2.5527, 5.8050),
(0.0000, 5.1053, 5.8050), (2.5527, 5.1053, 5.8050),
(5.1053, 5.1053, 5.8050), (7.6580, 5.1053, 5.8050),
(0.0000, 7.6580, 5.8050), (2.5527, 7.6580, 5.8050),
(5.1053, 7.6580, 5.8050), (7.6580, 7.6580, 5.8050),
(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
import numpy as np
from ase_ext import Atoms
from ase_ext.calculators.emt import EMT
from ase_ext.io import PickleTrajectory
Cu = Atoms('Cu', pbc=(1, 0, 0), calculator=EMT())
traj = PickleTrajectory('Cu.traj', 'w')
for a in np.linspace(2.0, 4.0, 20):
Cu.set_cell([a, 1, 1], scale_atoms=True)
traj.write(Cu)
def read_aims_output(filename, index=-1):
""" Import FHI-aims output files with all data available, i.e. relaxations,
MD information, force information etc etc etc. """
from ase_ext import Atoms, Atom
from ase_ext.calculators.singlepoint import SinglePointCalculator
from ase_ext.units import Ang, fs
molecular_dynamics = False
fd = open(filename, 'r')
cell = []
images = []
n_periodic = -1
f = None
pbc = False
found_aims_calculator = False
v_unit = Ang / (1000.0 * fs)
while True:
line = fd.readline()
if not line:
break
if "List of parameters used to initialize the calculator:" in line:
fd.readline()
calc = read_aims_calculator(fd)
calc.out = filename
found_aims_calculator = True
if "Number of atoms" in line:
inp = line.split()
n_atoms = int(inp[5])
if "| Unit cell:" in line:
if not pbc:
pbc = True
for i in range(3):
inp = fd.readline().split()
cell.append([inp[1], inp[2], inp[3]])
if "Atomic structure:" in line and not molecular_dynamics:
fd.readline()
atoms = Atoms()
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[3], (inp[4], inp[5], inp[6])))
if "Complete information for previous time-step:" in line:
molecular_dynamics = True
if "Updated atomic structure:" in line and not molecular_dynamics:
fd.readline()
atoms = Atoms()
velocities = []
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3])))
if molecular_dynamics:
inp = fd.readline().split()
if "Atomic structure (and velocities)" in line:
fd.readline()
atoms = Atoms()
velocities = []
for i in range(n_atoms):
inp = fd.readline().split()
atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3])))
inp = fd.readline().split()
velocities += [[
float(inp[1]) * v_unit,
float(inp[2]) * v_unit,
float(inp[3]) * v_unit
]]
atoms.set_velocities(velocities)
images.append(atoms)
if "Total atomic forces" in line:
f = []
for i in range(n_atoms):
inp = fd.readline().split()
f.append([float(inp[2]), float(inp[3]), float(inp[4])])
if not found_aims_calculator:
e = images[-1].get_potential_energy()
images[-1].set_calculator(
SinglePointCalculator(e, f, None, None, atoms))
e = None
f = None
if "Total energy corrected" in line:
e = float(line.split()[5])
if pbc:
atoms.set_cell(cell)
atoms.pbc = True
if not found_aims_calculator:
atoms.set_calculator(
SinglePointCalculator(e, None, None, None, atoms))
if not molecular_dynamics:
images.append(atoms)
e = None
if found_aims_calculator:
calc.set_results(images[-1])
images[-1].set_calculator(calc)
fd.close()
if molecular_dynamics:
images = images[1:]
# return requested images, code borrowed from ase_ext.io/trajectory.py
if isinstance(index, int):
return images[index]
else:
step = index.step or 1
if step > 0:
start = index.start or 0
if start < 0:
start += len(images)
stop = index.stop or len(images)
if stop < 0:
stop += len(images)
else:
if index.start is None:
start = len(images) - 1
else:
start = index.start
if start < 0:
start += len(images)
if index.stop is None:
stop = -1
else:
stop = index.stop
if stop < 0:
stop += len(images)
return [images[i] for i in range(start, stop, step)]
def read_aims(filename):
"""Import FHI-aims geometry type files.
Reads unitcell, atom positions and constraints from
a geometry.in file.
"""
from ase_ext import Atoms
from ase_ext.constraints import FixAtoms, FixCartesian
import numpy as np
atoms = Atoms()
fd = open(filename, 'r')
lines = fd.readlines()
fd.close()
positions = []
cell = []
symbols = []
fix = []
fix_cart = []
xyz = np.array([0, 0, 0])
i = -1
n_periodic = -1
periodic = np.array([False, False, False])
for n, line in enumerate(lines):
inp = line.split()
if inp == []:
continue
if inp[0] == 'atom':
if xyz.all():
fix.append(i)
elif xyz.any():
print(1)
fix_cart.append(FixCartesian(i, xyz))
floatvect = float(inp[1]), float(inp[2]), float(inp[3])
positions.append(floatvect)
symbols.append(inp[-1])
i += 1
xyz = np.array([0, 0, 0])
elif inp[0] == 'lattice_vector':
floatvect = float(inp[1]), float(inp[2]), float(inp[3])
cell.append(floatvect)
n_periodic = n_periodic + 1
periodic[n_periodic] = True
if inp[0] == 'constrain_relaxation':
if inp[1] == '.true.':
fix.append(i)
elif inp[1] == 'x':
xyz[0] = 1
elif inp[1] == 'y':
xyz[1] = 1
elif inp[1] == 'z':
xyz[2] = 1
if xyz.all():
fix.append(i)
elif xyz.any():
fix_cart.append(FixCartesian(i, xyz))
atoms = Atoms(symbols, positions)
if periodic.all():
atoms.set_cell(cell)
atoms.set_pbc(periodic)
if len(fix):
atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart)
else:
atoms.set_constraint(fix_cart)
return atoms
import numpy as np
from ase_ext.calculators.emt import EMT
from ase_ext import Atoms
a = 3.60
b = a / 2
cu = Atoms('Cu',
positions=[(0, 0, 0)],
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1,
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
cu.set_cell(cu.get_cell() * 1.001, scale_atoms=True)
e1 = cu.get_potential_energy()
V = a**3 / 4
B = 2 * (e1 - e0) / 0.003**2 / V * 160.2
print(B)
for i in range(4):
x = 0.001 * i
A = np.array([(x, b, b + x), (b, 0, b), (b, b, 0)])
cu.set_cell(A, scale_atoms=True)
e = cu.get_potential_energy() - e0
if i == 0:
print(i, e)
else:
print(i, e, e / x**2)
A = np.array([(0, b, b), (b, 0, b), (6 * b, 6 * b, 0)])
def read_vasp_out(filename='OUTCAR', index=-1):
"""Import OUTCAR type file.
Reads unitcell, atom positions, energies, and forces from the OUTCAR file.
- does not (yet) read any constraints
"""
import os
import numpy as np
from ase_ext.calculators.singlepoint import SinglePointCalculator
from ase_ext import Atoms, Atom
if isinstance(filename, str):
f = open(filename)
else: # Assume it's a file-like object
f = filename
data = f.readlines()
natoms = 0
images = []
atoms = Atoms(pbc=True)
energy = 0
species = []
species_num = []
symbols = []
for n, line in enumerate(data):
if 'POSCAR:' in line:
temp = line.split()
species = temp[1:]
if 'ions per type' in line:
temp = line.split()
for ispecies in range(len(species)):
species_num += [int(temp[ispecies + 4])]
natoms += species_num[-1]
for iatom in range(species_num[-1]):
symbols += [species[ispecies]]
if 'direct lattice vectors' in line:
cell = []
for i in range(3):
temp = data[n + 1 + i].split()
cell += [[float(temp[0]), float(temp[1]), float(temp[2])]]
atoms.set_cell(cell)
if 'FREE ENERGIE OF THE ION-ELECTRON SYSTEM' in line:
energy = float(data[n + 2].split()[4])
if 'POSITION ' in line:
forces = []
for iatom in range(natoms):
temp = data[n + 2 + iatom].split()
atoms += Atom(symbols[iatom],
[float(temp[0]),
float(temp[1]),
float(temp[2])])
forces += [[float(temp[3]), float(temp[4]), float(temp[5])]]
atoms.set_calculator(
SinglePointCalculator(energy, forces, None, None, atoms))
images += [atoms]
atoms = Atoms(pbc=True)
# return requested images, code borrowed from ase_ext.io/trajectory.py
if isinstance(index, int):
return images[index]
else:
step = index.step or 1
if step > 0:
start = index.start or 0
if start < 0:
start += len(images)
stop = index.stop or len(images)
if stop < 0:
stop += len(images)
else:
if index.start is None:
start = len(images) - 1
else:
start = index.start
if start < 0:
start += len(images)
if index.stop is None:
stop = -1
else:
stop = index.stop
if stop < 0:
stop += len(images)
return [images[i] for i in range(start, stop, step)]
# Distance between Cu atoms on a (100) surface:
d = 2.74
h1 = d * sqrt(3) / 2
h2 = d * sqrt(2.0 / 3)
initial = Atoms(
symbols='Pt',
positions=[
(0, 0, 0)
], #(1.37,0.79,2.24),(2.74,1.58,4.48),(0,0,6.72),(1.37,0.79,8.96),(2.74,1.58,11.2)],
cell=([(d, 0, 0), (d / 2, h1, 0), (d / 2, h1 / 3, -h2)]),
pbc=(True, True, True))
initial *= (7, 8, 6) # 5x5 (100) surface-cell
cell = initial.get_cell()
cell[2] = (0, 0, 22)
initial.set_cell(cell)
#initial.set_pbc((True,True,False))
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.2373
initial += Atom('Pt', (10.96, 11.074, h0))
initial += Atom('Pt', (13.7, 11.074, h0))
initial += Atom('Pt', (9.59, 8.701, h0))
initial += Atom('Pt', (12.33, 8.701, h0))
initial += Atom('Pt', (15.07, 8.701, h0))
initial += Atom('Pt', (10.96, 6.328, h0))
initial += Atom('Pt', (13.7, 6.328, h0))
if 0:
view(initial)
# Make band:
