def generate_database(dbfile, rc):
np.random.seed(123)
db = connect(dbfile)
rcov = covalent_radii[atomic_numbers['C']]
lc = 2 * np.sqrt(3) * rcov
slab = Graphene(symbol='C', latticeconstant=[lc, 12.]).repeat((3, 3, 1))
slab.center()
kwargs = {
'maximum_angular_momenta': mam,
'use_spline': False,
'Hamiltonian_SlaterKosterFiles_Suffix': '"_no_repulsion.skf"'
}
calc = DftbPlusCalc(slab, **kwargs)
slab.set_calculator(calc)
e_ref_slab = slab.get_potential_energy()
f_ref_slab = slab.get_forces()
m = molecule('N2')
m.positions += np.array([2.5, 3., 7.5])
for i in range(10):
print('Generating structure %d' % i)
n2 = m.copy()
for i, axis in enumerate('xyz'):
angle = np.random.random() * 180.
n2.rotate(angle, axis, center='COP')
calc = DftbPlusCalc(n2, **kwargs)
n2.set_calculator(calc)
e_ref_n2 = n2.get_potential_energy()
f_ref_n2 = n2.get_forces()
atoms = slab + n2
calc = DftbPlusCalc(atoms, **kwargs)
atoms.set_calculator(calc)
e = atoms.get_potential_energy()
f = atoms.get_forces()
e_rep, f_rep = calculate_target_repulsion(atoms, rc)
finalize(atoms, energy=e + e_rep, forces=f + f_rep, stress=None)
e_dft_ref = convert_array([e_ref_slab, e_ref_n2])
f_dft_ref = convert_array(np.vstack((f_ref_slab, f_ref_n2)))
db.write(atoms, relaxed=1, e_dft_ref=e_dft_ref, f_dft_ref=f_dft_ref)
return
# 5 x 5 supercell of graphene
index1 = 5
index2 = 5
a = 2.45
c = 3.355
gra = Graphene(symbol='C',
latticeconstant={
'a': a,
'c': c
},
size=(index1, index2, 1),
pbc=(1, 1, 0))
gra.center(vacuum=15.0, axis=2)
gra.center()
# Starting position of the projectile with an impact point at the
# center of a hexagon
projpos = [[gra[15].position[0], gra[15].position[1] + 1.41245, 25.0]]
H = Atoms('H', cell=gra.cell, positions=projpos)
# Combine target and projectile
atoms = gra + H
atoms.set_pbc(True)
# Specify the charge state of the projectile, either
# 0 (neutral) or 1 (singly charged ion)
charge = 0 # default for neutral projectile
import numpy as np
from ase.lattice.hexagonal import Graphene
from ase.parallel import parprint as pp
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
from gpaw.mpi import world
system = Graphene(symbol='C',
latticeconstant={'a': 2.45,'c': 1.0},
size=(1,1,1))
system.pbc = (1, 1, 0)
system.center(axis=2, vacuum=4.0)
nkpts = 5
communicator = world.new_communicator(np.array([world.rank]))
gpwname = 'dump.graphene.gpw'
if world.rank == 0:
calc = GPAW(mode='pw',
kpts=(nkpts, nkpts, 1),
communicator=communicator,
xc='oldLDA',
nbands=len(system) * 6,
txt='gpaw.graphene.txt')
system.set_calculator(calc)
system.get_potential_energy()
calc.write(gpwname, mode='all')
from ase.lattice.hexagonal import Graphene
# import ase.io as io
# from ase import Atoms, Atom
from ase.visualize import view
from ase.parallel import parprint as pp
from gpaw import GPAW, PW, restart
from gpaw.response.df import DielectricFunction
from gpaw.mpi import world
from gpaw.version import version
from ase.lattice import bulk
system = Graphene(symbol="C", latticeconstant={"a": 2.45, "c": 1.0}, size=(1, 1, 1))
system.pbc = (1, 1, 0)
system.center(axis=2, vacuum=4.0)
nkpts = 5
communicator = world.new_communicator(np.array([world.rank]))
gpwname = "dump.graphene.gpw"
if world.rank == 0:
calc = GPAW(
mode="pw",
kpts=(nkpts, nkpts, 1),
communicator=communicator,
xc="oldLDA",
nbands=len(system) * 6,
txt="gpaw.graphene.txt",
eigensolver='rmm-diis',
occupations=FermiDirac(0.001),
kpts={
'size': (6, 6, 1),
'gamma': True
})
layer = Graphene(symbol='B',
latticeconstant={
'a': 2.5,
'c': 1.0
},
size=(1, 1, 1))
layer[0].symbol = 'N'
layer.pbc = (1, 1, 0)
layer.center(axis=2, vacuum=4.0)
layer.set_calculator(calc)
layer.get_potential_energy()
nbecut = 50
from ase.units import Bohr, Hartree
vol = layer.get_volume() / Bohr**3
nbands = int(vol * (nbecut / Hartree)**1.5 * 2**0.5 / 3 / np.pi**2)
calc.diagonalize_full_hamiltonian(nbands)
calc.write('hBN.gpw', mode='all')
gw = G0W0('hBN.gpw',
'gw-hBN',
ecut=50,
domega0=0.1,