def get_dos(self, kpts=(10, 10, 10), npts=1000, delta=1e-3, indices=None):
from ase.spectrum.dosdata import RawDOSData
# dos = self.dos(kpts, npts, delta, indices)
kpts_kc = monkhorst_pack(kpts)
omega_w = self.band_structure(kpts_kc).ravel()
dos = RawDOSData(omega_w, np.ones_like(omega_w))
return dos
def get_dos(self, kpts=(10, 10, 10), npts=1000, delta=1e-3, indices=None):
#dos = self.dos(kpts, npts, delta, indices)
kpts_kc = monkhorst_pack(kpts)
omega_w = self.band_structure(kpts_kc).ravel()
from ase.dft.pdos import DOS
dos = DOS(omega_w, np.ones_like(omega_w)[None])
return dos
def dos(self, kpts=(10, 10, 10), npts=1000, delta=1e-3, indices=None):
"""Calculate phonon dos as a function of energy.
Parameters
----------
qpts: tuple
Shape of Monkhorst-Pack grid for sampling the Brillouin zone.
npts: int
Number of energy points.
delta: float
Broadening of Lorentzian line-shape in eV.
indices: list
If indices is not None, the atomic-partial dos for the specified
atoms will be calculated.
"""
# Monkhorst-Pack grid
kpts_kc = monkhorst_pack(kpts)
N = np.prod(kpts)
# Get frequencies
omega_kl = self.band_structure(kpts_kc)
# Energy axis and dos
omega_e = np.linspace(0., np.amax(omega_kl) + 5e-3, num=npts)
dos_e = np.zeros_like(omega_e)
# Sum up contribution from all q-points and branches
for omega_l in omega_kl:
diff_el = (omega_e[:, np.newaxis] - omega_l[np.newaxis, :])**2
dos_el = 1. / (diff_el + (0.5 * delta)**2)
dos_e += dos_el.sum(axis=1)
dos_e *= 1. / (N * pi) * 0.5 * delta
return omega_e, dos_e
def kpts2ndarray(kpts):
"""Convert kpts keyword to 2d ndarray of scaled k-points."""
if kpts is None:
return np.zeros((1, 3))
if isinstance(kpts[0], int):
return monkhorst_pack(kpts)
return np.array(kpts)
def dos(self, kpts=(10, 10, 10), npts=1000, delta=1e-3, indices=None):
"""Calculate phonon dos as a function of energy.
Parameters:
qpts: tuple
Shape of Monkhorst-Pack grid for sampling the Brillouin zone.
npts: int
Number of energy points.
delta: float
Broadening of Lorentzian line-shape in eV.
indices: list
If indices is not None, the atomic-partial dos for the specified
atoms will be calculated.
"""
# Monkhorst-Pack grid
kpts_kc = monkhorst_pack(kpts)
N = np.prod(kpts)
# Get frequencies
omega_kl = self.band_structure(kpts_kc)
# Energy axis and dos
omega_e = np.linspace(0., np.amax(omega_kl) + 5e-3, num=npts)
dos_e = np.zeros_like(omega_e)
# Sum up contribution from all q-points and branches
for omega_l in omega_kl:
diff_el = (omega_e[:, np.newaxis] - omega_l[np.newaxis, :])**2
dos_el = 1. / (diff_el + (0.5 * delta)**2)
dos_e += dos_el.sum(axis=1)
dos_e *= 1. / (N * pi) * 0.5 * delta
return omega_e, dos_e
def calculate_q(self, chi0, pd, chi0_swGG, chi0_swxvG, chi0_swvv, m1, m2,
cut_G, A2_x):
chi0_wGG = chi0_swGG[0]
if chi0_swxvG is not None:
chi0_wxvG = chi0_swxvG[0]
chi0_wvv = chi0_swvv[0]
else:
chi0_wxvG = None
chi0_wvv = None
chi0._calculate(pd,
chi0_wGG,
chi0_wxvG,
chi0_wvv,
m1,
m2,
spins='all',
extend_head=False)
print('E_c(q) = ', end='', file=self.fd)
chi0_wGG = chi0.redistribute(chi0_wGG, A2_x)
if not pd.kd.gamma:
e = self.calculate_energy(pd, chi0_wGG, cut_G)
print('%.3f eV' % (e * Hartree), file=self.fd)
self.fd.flush()
else:
from ase.dft import monkhorst_pack
kd = self.calc.wfs.kd
N = 4
N_c = np.array([N, N, N])
if self.truncation is not None:
N_c[kd.N_c == 1] = 1
q_qc = monkhorst_pack(N_c) / kd.N_c
q_qc *= 1.0e-6
U_scc = kd.symmetry.op_scc
q_qc = kd.get_ibz_q_points(q_qc, U_scc)[0]
weight_q = kd.q_weights
q_qv = 2 * np.pi * np.dot(q_qc, pd.gd.icell_cv)
nw = len(self.omega_w)
mynw = nw // self.nblocks
w1 = self.blockcomm.rank * mynw
w2 = w1 + mynw
a_qw = np.sum(np.dot(chi0_wvv[w1:w2], q_qv.T) * q_qv.T, axis=1).T
a0_qwG = np.dot(q_qv, chi0_wxvG[w1:w2, 0])
a1_qwG = np.dot(q_qv, chi0_wxvG[w1:w2, 1])
e = 0
for iq in range(len(q_qv)):
chi0_wGG[:, 0] = a0_qwG[iq]
chi0_wGG[:, :, 0] = a1_qwG[iq]
chi0_wGG[:, 0, 0] = a_qw[iq]
ev = self.calculate_energy(pd, chi0_wGG, cut_G, q_v=q_qv[iq])
e += ev * weight_q[iq]
print('%.3f eV' % (e * Hartree), file=self.fd)
self.fd.flush()
return e
def get_integrated_kernel(pd, N_c, truncation=None, N=100, reduced=False):
from scipy.special import j1, k0, j0, k1
B_cv = 2 * np.pi * pd.gd.icell_cv
Nf_c = np.array([N, N, N])
if reduced:
# Only integrate periodic directions if truncation is used
Nf_c[np.where(N_c == 1)[0]] = 1
q_qc = monkhorst_pack(Nf_c) / N_c
q_qc += pd.kd.ibzk_kc[0]
q_qv = np.dot(q_qc, B_cv)
if truncation is None:
V_q = 4 * np.pi / np.sum(q_qv**2, axis=1)
elif truncation == '2D':
# The non-periodic direction is determined from k-point grid
Nn_c = np.where(N_c == 1)[0]
Np_c = np.where(N_c != 1)[0]
if len(Nn_c) != 1:
# The k-point grid does not fit with boundary conditions
Nn_c = [2] # Choose reduced cell vectors 0, 1
Np_c = [0, 1] # Choose reduced cell vector 2
# Truncation length is half of cell vector in non-periodic direction
R = pd.gd.cell_cv[Nn_c[0], Nn_c[0]] / 2.
qp_q = ((q_qv[:, Np_c[0]])**2 + (q_qv[:, Np_c[1]]**2))**0.5
qn_q = q_qv[:, Nn_c[0]]
V_q = 4 * np.pi / (q_qv**2).sum(axis=1)
a_q = qn_q / qp_q * np.sin(qn_q * R) - np.cos(qn_q * R)
V_q *= 1. + np.exp(-qp_q * R) * a_q
elif truncation == '1D':
# The non-periodic direction is determined from k-point grid
Nn_c = np.where(N_c == 1)[0]
Np_c = np.where(N_c != 1)[0]
if len(Nn_c) != 2:
# The k-point grid does not fit with boundary conditions
Nn_c = [0, 1] # Choose reduced cell vectors 0, 1
Np_c = [2] # Choose reduced cell vector 2
# The radius is determined from area of non-periodic part of cell
Acell_cv = pd.gd.cell_cv[Nn_c, :][:, Nn_c]
R = (np.linalg.det(Acell_cv) / np.pi)**0.5
qnR_q = (q_qv[:, Nn_c[0]]**2 + q_qv[:, Nn_c[1]]**2)**0.5 * R
qpR_q = abs(q_qv[:, Np_c[0]]) * R
V_q = 4 * np.pi / (q_qv**2).sum(axis=1)
V_q *= (1.0 + qnR_q * j1(qnR_q) * k0(qpR_q) -
qpR_q * j0(qnR_q) * k1(qpR_q))
elif truncation == '0D' or 'wigner-seitz':
R = (3 * np.linalg.det(pd.gd.cell_cv) / (4 * np.pi))**(1. / 3.)
q2_q = (q_qv**2).sum(axis=1)
V_q = 4 * np.pi / q2_q
V_q *= 1.0 - np.cos(q2_q**0.5 * R)
return np.sum(V_q) / len(V_q), np.sum(V_q**0.5) / len(V_q)
def __init__(self, kpts, nspins):
"""Construct descriptor object for kpoint/spin combinations (ks-pair).
Parameters
----------
kpts: None, list of ints, or ndarray
Specification of the k-point grid. None=Gamma, list of
ints=Monkhorst-Pack, ndarray=user specified.
nspins: int
Number of spins.
Attributes
============ ======================================================
``N_c`` Number of k-points in the different directions.
``nspins`` Number of spins.
``nibzkpts`` Number of irreducible kpoints in 1st Brillouin zone.
``nks`` Number of k-point/spin combinations in total.
``mynks`` Number of k-point/spin combinations on this CPU.
``gamma`` Boolean indicator for gamma point calculation.
``comm`` MPI-communicator for kpoint distribution.
============ ======================================================
"""
if kpts is None:
self.bzk_kc = np.zeros((1, 3))
self.N_c = np.array((1, 1, 1), dtype=int)
elif isinstance(kpts[0], int):
self.bzk_kc = monkhorst_pack(kpts)
self.N_c = np.array(kpts, dtype=int)
else:
self.bzk_kc = np.array(kpts)
self.N_c = None
self.nspins = nspins
self.nbzkpts = len(self.bzk_kc)
# Gamma-point calculation
self.gamma = self.nbzkpts == 1 and not self.bzk_kc[0].any()
self.symmetry = None
self.comm = None
self.ibzk_kc = None
self.weight_k = None
self.nibzkpts = None
self.rank0 = None
self.mynks = None
self.ks0 = None
self.ibzk_qc = None
def get_phonons(self, kpts=(50, 50, 50), npts=5000):
"""Calculate the phonon spectrum and DOS.
Parameters
----------
kpts : tuple
Number of points in each directions of the k-space grid.
npts : int
Number of energy points to calculate the DOS at.
"""
self.phonons = Phonons(self.atoms,
self.calc(),
supercell=self.supercell_size,
delta=0.05,
name=self.name)
self.phonons.run()
# Read forces and assemble the dynamical matrix
self.phonons.read(acoustic=True)
self.phonon_kpts_mp = monkhorst_pack(kpts)
self.phonon_energy_mp = self.phonons.band_structure(
self.phonon_kpts_mp)
self.phonon_energy, self.phonon_dos = \
self.phonons.dos(kpts=kpts, npts=npts, delta=5e-4)
from __future__ import print_function
from ase import Atoms
from ase.build import bulk
from ase.dft import monkhorst_pack
from ase.parallel import paropen
from gpaw import GPAW, FermiDirac
from gpaw.wavefunctions.pw import PW
from gpaw.xc.exx import EXX
import numpy as np
# Monkhorst-Pack grid shifted to be gamma centered
k = 8
kpts = monkhorst_pack([k, k, k])
kpts += [1. / (2 * k), 1. / (2 * k), 1. / (2 * k)]
cell = bulk('C', 'fcc', a=3.553).get_cell()
a = Atoms('C2',
cell=cell,
pbc=True,
scaled_positions=((0, 0, 0), (0.25, 0.25, 0.25)))
calc = GPAW(mode=PW(600),
xc='PBE',
occupations=FermiDirac(width=0.01),
convergence={'density': 1.e-6},
kpts=kpts,
parallel={'domain': 1},
txt='diamond.ralda_01_pbe.txt')
a.set_calculator(calc)
E_pbe = a.get_potential_energy()
from ase.dft import monkhorst_pack assert [0, 0, 0] in monkhorst_pack((1, 3, 5)).tolist() assert [0, 0, 0] not in monkhorst_pack((1, 3, 6)).tolist() assert len(monkhorst_pack((3, 4, 6))) == 3 * 4 * 6 from ase.units import * print Hartree, Bohr, kJ/mol, kcal/mol, kB*300, fs, 1/fs
def calculate_screened_potential(self, ac):
"""Calculate W_GG(q)"""
chi0 = Chi0(self.calc,
frequencies=[0.0],
eta=0.001,
ecut=self.ecut,
intraband=False,
hilbert=False,
nbands=self.nbands,
txt='chi0.txt',
world=world,
)
self.blockcomm = chi0.blockcomm
wfs = self.calc.wfs
self.Q_qaGii = []
self.W_qGG = []
self.pd_q = []
t0 = time()
print('Calculating screened potential', file=self.fd)
for iq, q_c in enumerate(self.qd.ibzk_kc):
thisqd = KPointDescriptor([q_c])
pd = PWDescriptor(self.ecut, wfs.gd, complex, thisqd)
nG = pd.ngmax
chi0.Ga = self.blockcomm.rank * nG
chi0.Gb = min(chi0.Ga + nG, nG)
chi0_wGG = np.zeros((1, nG, nG), complex)
if np.allclose(q_c, 0.0):
chi0_wxvG = np.zeros((1, 2, 3, nG), complex)
chi0_wvv = np.zeros((1, 3, 3), complex)
else:
chi0_wxvG = None
chi0_wvv = None
chi0._calculate(pd, chi0_wGG, chi0_wxvG, chi0_wvv,
0, self.nbands, spins='all', extend_head=False)
chi0_GG = chi0_wGG[0]
# Calculate eps^{-1}_GG
if pd.kd.gamma:
# Generate fine grid in vicinity of gamma
kd = self.calc.wfs.kd
N = 4
N_c = np.array([N, N, N])
if self.truncation is not None:
# Only average periodic directions if trunction is used
N_c[kd.N_c == 1] = 1
qf_qc = monkhorst_pack(N_c) / kd.N_c
qf_qc *= 1.0e-6
U_scc = kd.symmetry.op_scc
qf_qc = kd.get_ibz_q_points(qf_qc, U_scc)[0]
weight_q = kd.q_weights
qf_qv = 2 * np.pi * np.dot(qf_qc, pd.gd.icell_cv)
a_q = np.sum(np.dot(chi0_wvv[0], qf_qv.T) * qf_qv.T, axis=0)
a0_qG = np.dot(qf_qv, chi0_wxvG[0, 0])
a1_qG = np.dot(qf_qv, chi0_wxvG[0, 1])
einv_GG = np.zeros((nG, nG), complex)
# W_GG = np.zeros((nG, nG), complex)
for iqf in range(len(qf_qv)):
chi0_GG[0] = a0_qG[iqf]
chi0_GG[:, 0] = a1_qG[iqf]
chi0_GG[0, 0] = a_q[iqf]
sqrV_G = get_coulomb_kernel(pd,
kd.N_c,
truncation=self.truncation,
wstc=self.wstc,
q_v=qf_qv[iqf])**0.5
sqrV_G *= ac**0.5 # Multiply by adiabatic coupling
e_GG = np.eye(nG) - chi0_GG * sqrV_G * sqrV_G[:,
np.newaxis]
einv_GG += np.linalg.inv(e_GG) * weight_q[iqf]
# einv_GG = np.linalg.inv(e_GG) * weight_q[iqf]
# W_GG += (einv_GG * sqrV_G * sqrV_G[:, np.newaxis]
# * weight_q[iqf])
else:
sqrV_G = get_coulomb_kernel(pd,
self.kd.N_c,
truncation=self.truncation,
wstc=self.wstc)**0.5
sqrV_G *= ac**0.5 # Multiply by adiabatic coupling
e_GG = np.eye(nG) - chi0_GG * sqrV_G * sqrV_G[:, np.newaxis]
einv_GG = np.linalg.inv(e_GG)
# W_GG = einv_GG * sqrV_G * sqrV_G[:, np.newaxis]
# Now calculate W_GG
if pd.kd.gamma:
# Reset bare Coulomb interaction
sqrV_G = get_coulomb_kernel(pd,
self.kd.N_c,
truncation=self.truncation,
wstc=self.wstc)**0.5
W_GG = einv_GG * sqrV_G * sqrV_G[:, np.newaxis]
if self.integrate_gamma != 0:
# Numerical integration of Coulomb interaction at all q-points
if self.integrate_gamma == 2:
reduced = True
else:
reduced = False
V0, sqrV0 = get_integrated_kernel(pd,
self.kd.N_c,
truncation=self.truncation,
reduced=reduced,
N=100)
W_GG[0, 0] = einv_GG[0, 0] * V0
W_GG[0, 1:] = einv_GG[0, 1:] * sqrV0 * sqrV_G[1:]
W_GG[1:, 0] = einv_GG[1:, 0] * sqrV_G[1:] * sqrV0
elif self.integrate_gamma == 0 and pd.kd.gamma:
# Analytical integration at gamma
bzvol = (2 * np.pi)**3 / self.vol / self.qd.nbzkpts
Rq0 = (3 * bzvol / (4 * np.pi))**(1. / 3.)
V0 = 16 * np.pi**2 * Rq0 / bzvol
sqrV0 = (4 * np.pi)**(1.5) * Rq0**2 / bzvol / 2
W_GG[0, 0] = einv_GG[0, 0] * V0
W_GG[0, 1:] = einv_GG[0, 1:] * sqrV0 * sqrV_G[1:]
W_GG[1:, 0] = einv_GG[1:, 0] * sqrV_G[1:] * sqrV0
else:
pass
if pd.kd.gamma:
e = 1 / einv_GG[0, 0].real
print(' RPA dielectric constant is: %3.3f' % e,
file=self.fd)
self.Q_qaGii.append(chi0.Q_aGii)
self.pd_q.append(pd)
self.W_qGG.append(W_GG)
if iq % (self.qd.nibzkpts // 5 + 1) == 2:
dt = time() - t0
tleft = dt * self.qd.nibzkpts / (iq + 1) - dt
print(' Finished %s q-points in %s - Estimated %s left' %
(iq + 1, timedelta(seconds=round(dt)),
timedelta(seconds=round(tleft))), file=self.fd)
def __init__(self,
calc=None,
spinors=False,
ecut=10.,
scale=1.0,
nbands=None,
valence_bands=None,
conduction_bands=None,
eshift=None,
gw_skn=None,
truncation=None,
integrate_gamma=1,
txt=sys.stdout,
mode='BSE',
wfile=None,
write_h=False,
write_v=False):
"""Creates the BSE object
calc: str or calculator object
The string should refer to the .gpw file contaning KS orbitals
ecut: float
Plane wave cutoff energy (eV)
nbands: int
Number of bands used for the screened interaction
valence_bands: list
Valence bands used in the BSE Hamiltonian
conduction_bands: list
Conduction bands used in the BSE Hamiltonian
eshift: float
Scissors operator opening the gap (eV)
gw_skn: list / array
List or array defining the gw quasiparticle energies used in
the BSE Hamiltonian. Should match spin, k-points and
valence/conduction bands
truncation: str
Coulomb truncation scheme. Can be either wigner-seitz,
2D, 1D, or 0D
integrate_gamma: int
Method to integrate the Coulomb interaction. 1 is a numerical
integration at all q-points with G=[0,0,0] - this breaks the
symmetry slightly. 0 is analytical integration at q=[0,0,0] only -
this conserves the symmetry. integrate_gamma=2 is the same as 1,
but the average is only carried out in the non-periodic directions.
txt: str
txt output
mode: str
Theory level used. can be RPA TDHF or BSE. Only BSE is screened.
wfile: str
File for saving screened interaction and some other stuff
needed later
write_h: bool
If True, write the BSE Hamiltonian to H_SS.ulm.
write_v: bool
If True, write eigenvalues and eigenstates to v_TS.ulm
"""
# Calculator
if isinstance(calc, str):
calc = GPAW(calc, txt=None, communicator=serial_comm)
self.calc = calc
self.spinors = spinors
self.scale = scale
assert mode in ['RPA', 'TDHF', 'BSE']
# assert calc.wfs.kd.nbzkpts % world.size == 0
# txt file
if world.rank != 0:
txt = devnull
elif isinstance(txt, str):
txt = open(txt, 'w', 1)
self.fd = txt
self.ecut = ecut / Hartree
self.nbands = nbands
self.mode = mode
self.truncation = truncation
if integrate_gamma == 0 and truncation is not None:
print('***WARNING*** Analytical Coulomb integration is ' +
'not expected to work with Coulomb truncation. ' +
'Use integrate_gamma=1', file=self.fd)
self.integrate_gamma = integrate_gamma
self.wfile = wfile
self.write_h = write_h
self.write_v = write_v
# Find q-vectors and weights in the IBZ:
self.kd = calc.wfs.kd
if -1 in self.kd.bz2bz_ks:
print('***WARNING*** Symmetries may not be right ' +
'Use gamma-centered grid to be sure', file=self.fd)
offset_c = 0.5 * ((self.kd.N_c + 1) % 2) / self.kd.N_c
bzq_qc = monkhorst_pack(self.kd.N_c) + offset_c
self.qd = KPointDescriptor(bzq_qc)
self.qd.set_symmetry(self.calc.atoms, self.kd.symmetry)
self.vol = abs(np.linalg.det(calc.wfs.gd.cell_cv))
# bands
self.spins = self.calc.wfs.nspins
if self.spins == 2:
if self.spinors:
self.spinors = False
print('***WARNING*** Presently the spinor version' +
'does not work for spin-polarized calculations.' +
'Performing scalar calculation', file=self.fd)
assert len(valence_bands[0]) == len(valence_bands[1])
assert len(conduction_bands[0]) == len(conduction_bands[1])
if valence_bands is None:
nv = self.calc.wfs.setups.nvalence
valence_bands = [[nv // 2 - 1]]
if self.spins == 2:
valence_bands *= 2
if conduction_bands is None:
conduction_bands = [[valence_bands[-1] + 1]]
if self.spins == 2:
conduction_bands *= 2
self.val_sn = np.array(valence_bands)
if len(np.shape(self.val_sn)) == 1:
self.val_sn = np.array([self.val_sn])
self.con_sn = np.array(conduction_bands)
if len(np.shape(self.con_sn)) == 1:
self.con_sn = np.array([self.con_sn])
self.td = True
for n in self.val_sn[0]:
if n in self.con_sn[0]:
self.td = False
if len(self.val_sn) == 2:
for n in self.val_sn[1]:
if n in self.con_sn[1]:
self.td = False
self.nv = len(self.val_sn[0])
self.nc = len(self.con_sn[0])
if eshift is not None:
eshift /= Hartree
if gw_skn is not None:
assert self.nv + self.nc == len(gw_skn[0, 0])
assert self.kd.nibzkpts == len(gw_skn[0])
gw_skn = gw_skn[:, self.kd.bz2ibz_k]
# assert self.kd.nbzkpts == len(gw_skn[0])
gw_skn /= Hartree
self.gw_skn = gw_skn
self.eshift = eshift
# Number of pair orbitals
self.nS = self.kd.nbzkpts * self.nv * self.nc * self.spins
self.nS *= (self.spinors + 1)**2
# Wigner-Seitz stuff
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.kd.N_c, self.fd)
else:
self.wstc = None
self.print_initialization(self.td, self.eshift, self.gw_skn)
from ase import *
from ase.lattice import bulk
from ase.dft import monkhorst_pack
from ase.parallel import paropen
from gpaw import *
from gpaw.wavefunctions.pw import PW
from gpaw.xc.exx import EXX
# Monkhorst-Pack grid shifted to be gamma centered
k = 8
kpts = monkhorst_pack([k, k, k])
kpts += [1. / (2 * k), 1. / ( 2 * k), 1. / (2 * k)]
cell = bulk('C', 'fcc', a=3.553).get_cell()
a = Atoms('C2', cell=cell, pbc=True,
scaled_positions=((0, 0, 0), (0.25, 0.25, 0.25)))
calc = GPAW(mode=PW(600),
xc='PBE',
occupations=FermiDirac(width=0.01),
convergence={'density': 1.e-6},
kpts=kpts,
txt='diamond_pbe.txt',
)
a.set_calculator(calc)
E_pbe = a.get_potential_energy()
exx = EXX(calc, txt='diamond_exx.txt')
exx.calculate()
E_hf = exx.get_total_energy()
from ase.dft import monkhorst_pack
assert [0, 0, 0] in monkhorst_pack((1, 3, 5)).tolist()
assert [0, 0, 0] not in monkhorst_pack((1, 3, 6)).tolist()
assert len(monkhorst_pack((3, 4, 6))) == 3 * 4 * 6
from ase.units import Hartree, Bohr, kJ, mol, kcal, kB, fs
print Hartree, Bohr, kJ/mol, kcal/mol, kB*300, fs, 1/fs
from ase.structure import bulk
ru = bulk('Ru', 'hcp', a=2.7) * (2, 2, 1)
assert abs(ru.get_distance(0, 7, mic=True) - ru.get_distance(1, 6)) < 1e-14
assert abs(ru.get_distance(0, 5, mic=True) - 2.7) < 1e-14
def kpts(self, kpts):
if not hasattr(self, '_kpts') or kpts != self._kpts:
self._kpts = kpts
self.kpts_kc = monkhorst_pack(self.kpts)
if hasattr(self, 'im_r'):
del self.im_r # we'll have to recalculate
old_cell = GR.get_cell()
old_cell[2, 2] = 2 * c
Graphite.set_cell(old_cell)
BNNB.set_pbc((True, True, True))
old_cell = BN.get_cell()
old_cell[2, 2] = 2 * c
BNNB.set_cell(old_cell)
BNNB.center()
GRBN.set_pbc((True, True, True))
old_cell = BN.get_cell()
old_cell[2, 2] = (NGr + NBN) * c
GRBN.set_cell(old_cell)
atoms = GRBN
from ase.dft import monkhorst_pack
calc = GPAW(
h=0.18,
mode=PW(600),
kpts=monkhorst_pack((29, 29, 1)) + np.array([0., 0., 0.]),
xc='PBE',
occupations=FermiDirac(0.01),
parallel={'band': 1},
)
atoms.set_calculator(calc)
ncpus = 16