def make_random_hbn_model(extent):
hbn = Graphene(symbol='N', latticeconstant={'a': 2.502, 'c': 12})
hbn[0].symbol = 'B'
rotation = np.random.rand() * 360
hbn.rotate(rotation, 'z', rotate_cell=True)
hbn = cut_rectangle(hbn, (0, 0), extent, margin=5)
return hbn
def get_ase_graphene(vacuum=5.0):
"""Get the ASE atoms for primitive (2-atom) graphene unit cell."""
from ase.lattice.hexagonal import Graphene
ase_atom = Graphene('C',
latticeconstant={
'a': 2.46 * A2B,
'c': vacuum * A2B
})
return ase_atom
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
from ase.units import Bohr
from gpaw.external import ConstantPotential
from gpaw import RMMDIIS
name = 'graphene_h'
# 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
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')
import numpy as np
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",
if 1:
calc = GPAW(mode='pw',
xc='PBE',
nbands=16,
setups={'Mo': '6'},
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')
import os
os.environ['LAMMPS_COMMAND'] = '/n/home08/xiey/lammps-16Mar18/src/lmp_mpi'
import numpy as np
from ase import Atoms, Atom
from ase.build import bulk, make_supercell
from ase.calculators.lammpsrun import LAMMPS
from ase.lattice.hexagonal import Graphene
symbol = 'C'
a = 2.46
c = 20.0 # vaccum
unit_cell = Graphene(symbol, latticeconstant={'a': a, 'c': c})
multiplier = np.array([[10, 0, 0], [0, 10, 0], [0, 0, 1]])
super_cell = make_supercell(unit_cell, multiplier)
nat = len(unit_cell.positions)
cell = np.array([[25.51020000000000, 0.00000000000000, 0.00000000000000],
[-12.75509999999999, 22.09248125562179, 0.00000000000000],
[0.00000000000000, 0.00000000000000, 20.00000000000000]])
super_cell.cell = cell
#a = [6.5, 6.5, 7.7]
#d = 2.3608
#NaCl = Atoms([Atom('Na', [0, 0, 0]),
# Atom('Cl', [0, 0, d])],
# cell=a, pbc=True)
pot_path = '/n/home08/xiey/lammps-16Mar18/potentials/'
parameters = {
'pair_style': 'airebo 3.0',