>>> d = 1.104 # N2 bondlength
>>> a = Atoms('N2', [(0, 0, 0), (0, 0, d)])
>>> a = Atoms(numbers=[7, 7], positions=[(0, 0, 0), (0, 0, d)])
>>> a = Atoms([Atom('N', (0, 0, 0)), Atom('N', (0, 0, d))])
so let's check"""
numbers = [7, 7]
symbols = ["N", "N"]
dummy_array = 2 * [3 * [0.0]]
d = 1.104 # N2 bondlength
a1 = Atoms("N2", [(0, 0, 0), (0, 0, d)])
a2 = Atoms(numbers=[7, 7], positions=[(0, 0, 0), (0, 0, d)])
a3 = Atoms([Atom("N", (0, 0, 0)), Atom("N", (0, 0, d))])
def test_atoms(atoms1=a1, atoms2=a2, atoms3=a3):
assert atoms1 == atoms2
assert atoms2 == atoms3
# test redundant keywords
def test_symbols(numbers=numbers, symbols=symbols):
kw = {"numbers": numbers, "symbols": symbols}
_test_keywords(**kw)
def test_momenta(numbers=numbers, momenta=dummy_array):
kw = {"momenta": momenta, "velocities": momenta}
def unitcell(self, latx, laty):
pos2 = np.array([
0.34109, 1.18154, 0, 7.16273, 4.33233, 0, 4.77515, 3.74156, 0,
5.11624, 2.36309, 0, 2.38758, 3.15078, 0, 5.45733, 6.10465, 0,
7.50382, 2.95387, 0, 3.41082, 4.13541, 0, 2.72866, 1.77231, 0,
0.68216, 4.92311, 0, 8.18599, 5.31696, 0, 4.09299, 1.37846, 0,
8.18599, 0.19692, 0, 6.82166, 0.59078, 0, 2.04649, 14.76931, 0,
3.41082, 14.37546, 0, 5.45733, 11.22468, 0, 1.36433, 12.40622, 0,
0.68216, 10.04313, 0, 0.34109, 11.42161, 0, 6.13949, 13.58776, 0,
3.06975, 10.6339, 0, 2.72866, 12.01237, 0, 7.8449, 11.81546, 0,
5.11624, 12.60315, 0, 7.50382, 13.19392, 0, 8.52706, 9.0585, 0,
6.82166, 10.83083, 0, 6.48057, 7.08926, 0, 3.75191, 7.87696, 0,
4.77515, 8.86159, 0, 6.13949, 8.46774, 0, 1.70542, 5.90772, 0,
1.36433, 7.2862, 0, 4.09299, 6.4985, 0, 2.04649, 9.64928, 0, 0,
2.56002, 0, 0, 7.68004, 0, 9.8914, 3.54463, 0, 14.66656, 4.72618,
0, 13.6433, 3.74156, 0, 14.32548, 6.10465, 0, 16.37197, 2.95387, 0,
11.9379, 5.51387, 0, 12.27897, 4.13541, 0, 11.59681, 1.77231, 0,
9.55032, 4.92311, 0, 17.05414, 5.31696, 0, 16.71305, 6.69542, 0,
12.96114, 1.37846, 0, 10.57357, 0.7877, 0, 17.05414, 0.19692, 0,
15.34872, 1.96924, 0, 15.68981, 0.59078, 0, 10.91464, 14.76931, 0,
17.39521, 14.17854, 0, 12.27897, 14.37546, 0, 14.32548, 11.22468,
0, 12.62006, 12.997, 0, 10.23248, 12.40622, 0, 9.8914, 13.7847, 0,
9.55032, 10.04313, 0, 15.00764, 13.58776, 0, 11.59681, 12.01237, 0,
14.66656, 14.96624, 0, 16.37197, 13.19392, 0, 15.68981, 10.83083,
0, 13.6433, 8.86159, 0, 15.00764, 8.46774, 0, 16.03088, 9.45235, 0,
10.23248, 7.2862, 0, 12.96114, 6.4985, 0, 11.25573, 8.27081, 0,
10.91464, 9.64928, 0, 8.86815, 2.56002, 0, 8.86815, 7.68004, 0,
13.30223, 0, 0, 13.30223, 10.24006, 0, 1.02325, 18.90472, 0,
5.7984, 20.08626, 0, 4.77515, 19.10165, 0, 5.45733, 21.46474, 0,
7.50382, 18.31395, 0, 3.06975, 20.87396, 0, 3.41082, 19.4955, 0,
2.72866, 17.1324, 0, 0.68216, 20.28319, 0, 8.18599, 20.67704, 0,
7.8449, 22.0555, 0, 4.09299, 16.73855, 0, 1.70542, 16.14778, 0,
8.18599, 15.557, 0, 6.48057, 17.32933, 0, 6.82166, 15.95087, 0,
2.04649, 30.12939, 0, 8.52706, 29.53863, 0, 3.41082, 29.73555, 0,
5.45733, 26.58476, 0, 3.75191, 28.35709, 0, 1.36433, 27.76631, 0,
1.02325, 29.14478, 0, 0.68216, 25.40322, 0, 6.13949, 28.94785, 0,
2.72866, 27.37246, 0, 5.7984, 30.32633, 0, 7.50382, 28.554, 0,
6.82166, 26.19091, 0, 4.77515, 24.22167, 0, 6.13949, 23.82783, 0,
7.16273, 24.81244, 0, 1.36433, 22.64628, 0, 4.09299, 21.85859, 0,
2.38758, 23.6309, 0, 2.04649, 25.00937, 0, 0, 17.92011, 0, 0,
23.04013, 0, 4.43408, 15.36009, 0, 4.43408, 25.60015, 0, 9.20924,
16.54163, 0, 16.03088, 19.69242, 0, 13.6433, 19.10165, 0, 13.98439,
17.72318, 0, 11.25573, 18.51087, 0, 14.32548, 21.46474, 0,
16.37197, 18.31395, 0, 12.27897, 19.4955, 0, 11.59681, 17.1324, 0,
9.55032, 20.28319, 0, 17.05414, 20.67704, 0, 12.96114, 16.73855, 0,
17.05414, 15.557, 0, 15.68981, 15.95087, 0, 10.91464, 30.12939, 0,
12.27897, 29.73555, 0, 14.32548, 26.58476, 0, 10.23248, 27.76631,
0, 9.55032, 25.40322, 0, 9.20924, 26.78169, 0, 15.00764, 28.94785,
0, 11.9379, 25.99398, 0, 11.59681, 27.37246, 0, 16.71305, 27.17554,
0, 13.98439, 27.96324, 0, 16.37197, 28.554, 0, 17.39521, 24.41859,
0, 15.68981, 26.19091, 0, 15.34872, 22.44935, 0, 12.62006,
23.23705, 0, 13.6433, 24.22167, 0, 15.00764, 23.82783, 0, 10.57357,
21.26781, 0, 10.23248, 22.64628, 0, 12.96114, 21.85859, 0,
10.91464, 25.00937, 0, 8.86815, 17.92011, 0, 8.86815, 23.04013, 0,
1.02325, 3.54463, 0, 5.7984, 4.72618, 0, 3.06975, 5.51387, 0,
7.8449, 6.69542, 0, 1.70542, 0.7877, 0, 6.48057, 1.96924, 0,
8.52706, 14.17854, 0, 3.75191, 12.997, 0, 1.02325, 13.7847, 0,
5.7984, 14.96624, 0, 7.16273, 9.45235, 0, 2.38758, 8.27081, 0,
4.43408, 0, 0, 4.43408, 10.24006, 0, 9.20924, 1.18154, 0, 16.03088,
4.33233, 0, 13.98439, 2.36309, 0, 11.25573, 3.15078, 0, 9.20924,
11.42161, 0, 11.9379, 10.6339, 0, 16.71305, 11.81546, 0, 13.98439,
12.60315, 0, 17.39521, 9.0585, 0, 15.34872, 7.08926, 0, 12.62006,
7.87696, 0, 10.57357, 5.90772, 0, 0.34109, 16.54163, 0, 7.16273,
19.69242, 0, 5.11624, 17.72318, 0, 2.38758, 18.51087, 0, 0.34109,
26.78169, 0, 3.06975, 25.99398, 0, 7.8449, 27.17554, 0, 5.11624,
27.96324, 0, 8.52706, 24.41859, 0, 6.48057, 22.44935, 0, 3.75191,
23.23705, 0, 1.70542, 21.26781, 0, 9.8914, 18.90472, 0, 14.66656,
20.08626, 0, 11.9379, 20.87396, 0, 16.71305, 22.0555, 0, 10.57357,
16.14778, 0, 15.34872, 17.32933, 0, 17.39521, 29.53863, 0,
12.62006, 28.35709, 0, 9.8914, 29.14478, 0, 14.66656, 30.32633, 0,
16.03088, 24.81244, 0, 11.25573, 23.6309, 0, 13.30223, 15.36009, 0,
13.30223, 25.60015, 0
]).reshape(-1, 3) / 1.42
pos1 = [6.928400, 13.000369, 0.000000, 7.794450, 16.500469, 0.000000]
phi = pi / 2 - atan((pos1[4] - pos1[1]) / (pos1[3] - pos1[0]))
cbond = np.linalg.norm((pos1[4] - pos1[1], pos1[3] - pos1[0], 0))
dx = sqrt(3) * cbond * 2
dy = 3 * cbond * 2
atoms = Atoms()
for i, coord in enumerate(pos2):
ele = ['C', 'N'][i < 156]
atom = Atom(ele, coord)
atoms.append(atom)
#atoms.rotate('z',phi)
atoms.set_cell([dx, dy, 10.0])
col = atoms.repeat((latx, laty, 1))
return col
from jasp import *
from ase import Atom, Atoms
from ase.io import write
from enthought.mayavi import mlab
from ase.data import vdw_radii
from ase.data.colors import cpk_colors
atoms = Atoms([
Atom('C', [0.0000, 0.0000, -0.8088]),
Atom('Br', [0.0000, 0.0000, 1.1146]),
Atom('F', [0.0000, 1.2455, -1.2651]),
Atom('F', [1.0787, -0.6228, -1.2651]),
Atom('F', [-1.0787, -0.6228, -1.2651])
],
cell=(10, 10, 10))
atoms.center()
with jasp('molecules/CF3Br',
encut=350,
xc='PBE',
ibrion=1,
nsw=50,
lvtot=True,
lvhar=True,
atoms=atoms) as calc:
calc.set_nbands(f=2)
calc.calculate()
x, y, z, lp = calc.get_local_potential()
x, y, z, cd = calc.get_charge_density()
mlab.figure(1, bgcolor=(1, 1, 1)) # make a white figure
# plot the atoms as spheres
for atom in atoms:
mlab.points3d(
from ase.test import NotAvailable
import numpy as np
import ase.io.netcdftrajectory as netcdftrajectory
if not netcdftrajectory.have_nc:
raise NotAvailable('No NetCDF module available (netCDF4-python, '
'scipy.io.netcdf)')
import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory
co = Atoms([Atom('C', (0, 0, 0)), Atom('O', (0, 0, 1.2))],
cell=[3, 3, 3],
pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
traj = NetCDFTrajectory('1.nc', 'a')
co = traj[-1]
print(co.positions)
co.positions[:] += 1
traj.write(co)
del traj
t = NetCDFTrajectory('1.nc', 'a')
else:
t = NetCDFTrajectory('1.nc', 'r')
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.05
d = a / 2**0.5
bulk = Atoms([Atom('Al', (0, 0, 0)), Atom('Al', (0.5, 0.5, 0.5))], pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h, nbands=2 * 8, kpts=(2, 2, 2), convergence={'energy': 1e-5})
bulk.set_calculator(calc)
e0 = bulk.get_potential_energy()
niter0 = calc.get_number_of_iterations()
calc = GPAW(h=h,
nbands=2 * 8,
kpts=(2, 2, 2),
convergence={'energy': 1e-5},
eigensolver='cg')
bulk.set_calculator(calc)
e1 = bulk.get_potential_energy()
niter1 = calc.get_number_of_iterations()
equal(e0, e1, 3.6e-5)
energy_tolerance = 0.00004
niter_tolerance = 0
equal(e0, -6.97626, energy_tolerance)
assert 16 <= niter0 <= 22, niter0
equal(e1, -6.97627, energy_tolerance)
assert 12 <= niter1 <= 17, niter1
# 12-ZGNR with adsorbed H at both edges.
# "ZGNR12.py" should be run first!
from ase.io import read
from ase import Atom
from ase.structure import graphene_nanoribbon
from ase.optimize import QuasiNewton
from gpaw import GPAW
GNR = read('ZGNR12.traj')
pos = GNR[22].get_position() + [-1.05, 0.0, 0.0]
GNR.append(Atom('H', pos))
pos = GNR[1].get_position() + [1.05, 0.0, 0.0]
GNR.append(Atom('H', pos))
GNR.set_pbc((0, 0, 1))
kpts = (1, 1, 10)
calc = GPAW(kpts=kpts, spinpol=True)
GNR.set_calculator(calc)
dyn = QuasiNewton(GNR, trajectory='GNR_H.traj')
dyn.run(fmax=0.05)
from math import pi, cos, sin
from ase import Atom, Atoms
from ase.parallel import rank, barrier
from gpaw import GPAW
from gpaw.test import equal, gen
import numpy as np
# Generate setup for oxygen with half a core-hole:
gen('O', name='hch1s', corehole=(1, 0, 0.5))
if 1:
a = 5.0
d = 0.9575
t = pi / 180 * 104.51
H2O = Atoms([
Atom('O', (0, 0, 0)),
Atom('H', (d, 0, 0)),
Atom('H', (d * cos(t), d * sin(t), 0))
],
cell=(a, a, a),
pbc=False)
H2O.center()
calc = GPAW(nbands=10, h=0.2, setups={'O': 'hch1s'})
H2O.set_calculator(calc)
e = H2O.get_potential_energy()
niter = calc.get_number_of_iterations()
calc.write('h2o.gpw')
else:
calc = GPAW('h2o.gpw')
calc.initialize_positions()
from ase import Atoms, Atom
from ase.io import write
# define an Atoms object
atoms = Atoms([Atom('C', [0., 0., 0.]),
Atom('O', [1.1, 0., 0.])],
cell=(10, 10, 10))
print 'V = {0:1.0f} Angstrom^3'.format(atoms.get_volume())
write('images/simple-cubic-cell.png', atoms, show_unit_cell=2)
import numpy as np
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
from gpaw.lrtddft import LrTDDFT
txt = '-'
txt = None
load = True
load = False
R = 0.7 # approx. experimental bond length
a = 4.0
c = 5.0
H2 = Atoms([
Atom('H', (a / 2, a / 2, (c - R) / 2)),
Atom('H', (a / 2, a / 2, (c + R) / 2))
],
cell=(a, a, c))
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
calc.write('H2saved_wfs.gpw', 'all')
calc.write('H2saved.gpw')
wfs_error = calc.wfs.eigensolver.error
xc = 'LDA'
#print "-> starting directly after a gs calculation"
lr = LrTDDFT(calc, xc=xc, txt='-')
from ase.constraints import FixAtoms
from matplotlib import mlab
from numpy import *
from ase.utils.eos import EquationOfState
from ase.lattice.cubic import BodyCenteredCubic
from ase import Atom
a = 5.7885 / 2
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5, 5])
atoms.set_cell([a, a, a], scale_atoms=True)
#atoms.set_cell([a,a,a])
carbon = Atom('C', position=(0, 0.5 * a, 0.5 * a), charge=0.4)
atoms = atoms * (2, 2, 2) + carbon
constraint = FixAtoms(indices=[8, 10])
atoms.set_constraint(constraint)
init = atoms.copy()
final = atoms.copy()
final[-1].position = [0, 0.5 * a, (0.5 + 0.25) * a]
for i in range(0, 18):
os.system('mkdir {:02d}'.format(i))
os.chdir('{:02d}'.format(i))