def check_df(name, ref_energy, ref_loss, ref_energy_lfe, ref_loss_lfe,
**kwargs_override):
kwargs = dict(calc=calc, q=q, w=w.copy(), eta=0.5, ecut=(30, 30, 30),
txt='df.%s.txt' % name)
kwargs.update(kwargs_override)
df = DF(**kwargs)
fname = 'dfdump.%s.dat' % name
df.get_EELS_spectrum(filename=fname)
world.barrier()
d = np.loadtxt(fname)
loss = d[:, 1]
loss_lfe = d[:, 2]
energies = d[:, 0]
#import pylab as pl
#fig = pl.figure()
#ax1 = fig.add_subplot(111)
#ax1.plot(d[:, 0], d[:, 1]/np.max(d[:, 1]))
#ax1.plot(d[:, 0], d[:, 2]/np.max(d[:, 2]))
#ax1.axis(ymin=0, ymax=1)
#fig.savefig('fig.%s.pdf' % name)
energy, peakloss = getpeak(energies, loss)
energy_lfe , peakloss_lfe = getpeak(energies, loss_lfe)
check(name, energy, peakloss, ref_energy, ref_loss)
check('%s-lfe' % name, energy_lfe, peakloss_lfe, ref_energy_lfe,
ref_loss_lfe)
line = template % (name, energy, peakloss, energy_lfe, peakloss_lfe,
repr(kwargs_override))
scriptlines.append(line)
def full_static_screened_interaction(self):
"""Calcuate W_GG(q)"""
W_qGG = np.zeros((self.nibzq, self.npw, self.npw), dtype=complex)
t0 = time()
for iq in range(self.nibzq):
q = self.ibzq_qc[iq]
optical_limit = False
if np.abs(q).sum() < 1e-8:
q = self.q_c.copy()
optical_limit = True
df = DF(calc=self.calc,
q=q,
w=(0.,),
optical_limit=optical_limit,
nbands=self.nbands,
hilbert_trans=False,
eta=0.0001,
ecut=self.ecut*Hartree,
xc='RPA',
txt='df.out')
df.initialize()
df.calculate()
if optical_limit:
K_GG = self.V_qGG[iq].copy()
q_v = np.dot(q, self.bcell_cv)
K0 = calculate_Kc(q,
self.Gvec_Gc,
self.acell_cv,
self.bcell_cv,
self.pbc,
vcut=self.vcut)[0,0]
for iG in range(1,self.npw):
K_GG[0, iG] = self.V_qGG[iq, iG, iG]**0.5 * K0**0.5
K_GG[iG, 0] = self.V_qGG[iq, iG, iG]**0.5 * K0**0.5
K_GG[0,0] = K0
df_GG = np.eye(self.npw, self.npw) - K_GG*df.chi0_wGG[0]
else:
df_GG = np.eye(self.npw, self.npw) - self.V_qGG[iq]*df.chi0_wGG[0]
dfinv_GG = np.linalg.inv(df_GG)
if optical_limit:
eps = 1/dfinv_GG[0,0]
self.printtxt(' RPA macroscopic dielectric constant is: %3.3f' % eps.real)
W_qGG[iq] = dfinv_GG * self.V_qGG[iq]
self.timing(iq, t0, self.nibzq, 'iq')
if rank == 0:
if self.kernel_file is not None:
data = {'W_qGG': W_qGG}
name = self.kernel_file+'.pckl'
pickle.dump(data, open(name, 'w'), -1)
return W_qGG
def initialize_calculation(self, w, ecut, nbands, kcommsize, extrapolate):
dummy = DF(calc=self.calc,
eta=0.0,
w=w * 1j,
q=[0.,0.,0.],
ecut=ecut,
hilbert_trans=False,
kcommsize=kcommsize)
dummy.txt = devnull
dummy.spin = 0
dummy.initialize()
if nbands is None:
nbands = dummy.npw
self.nbands = nbands
print >> self.txt, 'Planewave cut off : %s eV' % ecut
print >> self.txt, 'Number of Planewaves : %s' % dummy.npw
print >> self.txt, 'Response function bands : %s' % nbands
print >> self.txt, 'Frequency range : %s - %s eV' % (w[0], w[-1])
print >> self.txt, 'Number of frequency points : %s' % len(w)
if extrapolate:
print >> self.txt, 'Extrapolation of frequencies : Squared Lorentzian'
print >> self.txt
print >> self.txt, 'Parallelization scheme'
print >> self.txt, ' Total cpus : %d' % dummy.comm.size
if dummy.nkpt == 1:
print >> self.txt, ' Band parsize : %d' % dummy.kcomm.size
else:
print >> self.txt, ' Kpoint parsize : %d' % dummy.kcomm.size
print >> self.txt, ' Frequency parsize : %d' % dummy.wScomm.size
print >> self.txt, 'Memory usage estimate'
print >> self.txt, ' chi0_wGG(Q) : %f M / cpu' % (dummy.Nw_local *
dummy.npw**2 * 16.
/ 1024**2)
print >> self.txt
del dummy
def initialize_calculation(self, w, ecut, nbands, kcommsize, extrapolate):
dummy = DF(calc=self.calc,
eta=0.0,
w=w * 1j,
q=[0., 0., 0.],
ecut=ecut,
hilbert_trans=False,
kcommsize=kcommsize)
dummy.txt = devnull
dummy.spin = 0
dummy.initialize()
if nbands is None:
nbands = dummy.npw
self.nbands = nbands
print >> self.txt, 'Planewave cut off : %s eV' % ecut
print >> self.txt, 'Number of Planewaves : %s' % dummy.npw
print >> self.txt, 'Response function bands : %s' % nbands
print >> self.txt, 'Frequency range : %s - %s eV' % (
w[0], w[-1])
print >> self.txt, 'Number of frequency points : %s' % len(w)
if extrapolate:
print >> self.txt, 'Extrapolation of frequencies : Squared Lorentzian'
print >> self.txt
print >> self.txt, 'Parallelization scheme'
print >> self.txt, ' Total cpus : %d' % dummy.comm.size
if dummy.nkpt == 1:
print >> self.txt, ' Band parsize : %d' % dummy.kcomm.size
else:
print >> self.txt, ' Kpoint parsize : %d' % dummy.kcomm.size
print >> self.txt, ' Frequency parsize : %d' % dummy.wScomm.size
print >> self.txt, 'Memory usage estimate'
print >> self.txt, ' chi0_wGG(Q) : %f M / cpu' % (
dummy.Nw_local * dummy.npw**2 * 16. / 1024**2)
print >> self.txt
del dummy
def E_q(self,
q,
index=None,
direction=0,
integrated=True):
if abs(np.dot(q, q))**0.5 < 1.e-5:
q = [0.,0.,0.]
q[direction] = 1.e-5
optical_limit = True
else:
optical_limit = False
dummy = DF(calc=self.calc,
eta=0.0,
w=self.w * 1j,
q=q,
ecut=self.ecut,
G_plus_q=True,
optical_limit=optical_limit,
hilbert_trans=False)
dummy.txt = devnull
dummy.initialize(simple_version=True)
npw = dummy.npw
del dummy
if self.nbands is None:
nbands = npw
else:
nbands = self.nbands
if self.txt is sys.stdout:
txt = 'response.txt'
else:
txt='response_'+self.txt.name
df = DF(calc=self.calc,
xc=None,
nbands=nbands,
eta=0.0,
q=q,
txt=txt,
vcut=self.vcut,
w=self.w * 1j,
ecut=self.ecut,
G_plus_q=True,
kcommsize=self.kcommsize,
comm=self.dfcomm,
optical_limit=optical_limit,
hilbert_trans=False)
if index is None:
print >> self.txt, 'Calculating KS response function at:'
else:
print >> self.txt, '#', index, \
'- Calculating KS response function at:'
if optical_limit:
print >> self.txt, 'q = [0 0 0] -', 'Polarization: ', direction
else:
print >> self.txt, 'q = [%1.6f %1.6f %1.6f] -' \
% (q[0],q[1],q[2]), '%s planewaves' % npw
e_wGG = df.get_dielectric_matrix(xc='RPA', overwritechi0=True)
df.chi0_wGG = None
Nw_local = len(e_wGG)
local_E_q_w = np.zeros(Nw_local, dtype=complex)
E_q_w = np.empty(len(self.w), complex)
for i in range(Nw_local):
local_E_q_w[i] = (np.log(np.linalg.det(e_wGG[i]))
+ len(e_wGG[0]) - np.trace(e_wGG[i]))
#local_E_q_w[i] = (np.sum(np.log(np.linalg.eigvals(e_wGG[i])))
# + len(e_wGG[0]) - np.trace(e_wGG[i]))
df.wcomm.all_gather(local_E_q_w, E_q_w)
del df
if self.gauss_legendre is not None:
E_q = np.sum(E_q_w * self.gauss_weights * self.transform) \
/ (4*np.pi)
else:
dws = self.w[1:] - self.w[:-1]
E_q = np.dot((E_q_w[:-1] + E_q_w[1:])/2., dws) / (2.*np.pi)
print >> self.txt, 'E_c(q) = %s eV' % E_q.real
print >> self.txt
if integrated:
return E_q.real
else:
return E_q_w.real
eigensolver=
'cg', # It's preferable to use 'cg' to calculate unoccupied states.
occupations=FermiDirac(0.05),
txt='out_gs.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('graphite.gpw', 'all')
# Part 2: Spectra calculations
f = paropen('graphite_q_list', 'w') # Write down q.
for i in range(1, 8): # Loop over different q.
df = DF(
calc='graphite.gpw',
nbands=60, # Use only bands that are converged in the gs calculation.
q=np.array([i / 20., 0., 0.]), # Gamma - M excitation
#q=np.array([i/20., -i/20., 0.]) # Gamma - K excitation
w=np.linspace(0, 40, 401), # Spectra from 0-40 eV with 0.1 eV spacing.
eta=0.2, # Broadening parameter.
ecut=40 + (i - 1) *
10, # In general, larger q requires larger planewave cutoff energy. #
txt='out_df_%d.txt' % (i)) # Write differnt output for different q.
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2, filename='graphite_EELS_%d' %
(i)) # Use different filenames for different q
df.check_sum_rule(df1, df2) # Check f-sum rule.
print >> f, sqrt(np.inner(df.qq_v / Bohr, df.qq_v / Bohr))
nc=[0,4],
coupling=True,
mode='RPA',
q=np.array([0.25, 0, 0]),
ecut=50.,
eta=0.2)
bse.get_dielectric_function('Al_bse.dat')
if df:
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al.gpw',
q=q,
w=w,
eta=0.2,
ecut=50,
hilbert_trans=False)
df.get_EELS_spectrum(filename='Al_df.dat')
df.write('Al.pckl')
df.check_sum_rule()
if check_spectrum:
d = np.loadtxt('Al_bse.dat')[:,2]
wpeak = 16.4
Nw = 164
if d[Nw] > d[Nw-1] and d[Nw] > d[Nw+1]:
pass
else:
raise ValueError('Plasmon peak not correct ! ')
# GS Calculation One
a = 6.75 * Bohr
atoms = bulk("C", "diamond", a=a)
calc = GPAW(h=0.2, eigensolver=RMM_DIIS(), mixer=Mixer(0.1, 3), kpts=(4, 4, 4), occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write("C.gpw", "all")
# Macroscopic dielectric constant calculation
q = np.array([0.0, 0.00001, 0.0])
w = np.linspace(0, 24.0, 241)
df = DF(calc="C.gpw", q=q, w=(0.0,), eta=0.001, ecut=50, hilbert_trans=False, optical_limit=True)
eM1, eM2 = df.get_macroscopic_dielectric_constant()
eM1_ = 6.15176021 # 6.15185095143 for dont use time reversal symmetry
eM2_ = 6.04805705 # 6.04815084635
if np.abs(eM1 - eM1_) > 1e-5 or np.abs(eM2 - eM2_) > 1e-5:
print eM1, eM2
raise ValueError("Macroscopic dielectric constant not correct ! ")
# Absorption spectrum calculation
del df
df = DF(calc="C.gpw", q=q, w=w, eta=0.25, ecut=50, optical_limit=True, txt="C_df.out")
df.get_absorption_spectrum()
df.check_sum_rule()
convergence={'bands':60}, # It's better NOT to converge all bands.
eigensolver='cg', # It's preferable to use 'cg' to calculate unoccupied states.
occupations=FermiDirac(0.05),
txt='out_gs.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('graphite.gpw','all')
# Part 2: Spectra calculations
f = paropen('graphite_q_list', 'w') # Write down q.
for i in range(1,8): # Loop over different q.
df = DF(calc='graphite.gpw',
nbands=60, # Use only bands that are converged in the gs calculation.
q=np.array([i/20., 0., 0.]), # Gamma - M excitation
#q=np.array([i/20., -i/20., 0.]) # Gamma - K excitation
w=np.linspace(0, 40, 401), # Spectra from 0-40 eV with 0.1 eV spacing.
eta=0.2, # Broadening parameter.
ecut=40+(i-1)*10, # In general, larger q requires larger planewave cutoff energy. #
txt='out_df_%d.txt' %(i)) # Write differnt output for different q.
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2, filename='graphite_EELS_%d' %(i)) # Use different filenames for different q
df.check_sum_rule(df1, df2) # Check f-sum rule.
print >> f, sqrt(np.inner(df.qq_v / Bohr, df.qq_v / Bohr))
occupations=FermiDirac(0.001),
convergence={'bands': 70})
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('si.gpw', 'all')
if ABS:
w = np.linspace(0, 24, 481)
q = np.array([0.0, 0.00001, 0.])
# getting macroscopic constant
df = DF(calc='si.gpw',
q=q,
w=(0., ),
eta=0.0001,
hilbert_trans=False,
txt='df_1.out',
ecut=150,
optical_limit=True)
df1, df2 = df.get_dielectric_function()
eM1, eM2 = df.get_macroscopic_dielectric_constant(df1, df2)
df.write('df_1.pckl')
if np.abs(eM1 - 13.992277) > 1e-4 or np.abs(eM2 - 12.589596) > 1e-4:
print eM1, eM2
raise ValueError('Pls check dielectric constant !')
#getting absorption spectrum
df = DF(calc='si.gpw',
kpts=(4,4,4),
mode='lcao',
basis='dzp',
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al.gpw','all')
t2 = time.time()
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al.gpw', q=q, w=w, eta=0.2, ecut=50)
df1, df2 = df.get_dielectric_function()
#df.write('Al.pckl')
df.get_EELS_spectrum(df1, df2,filename='EELS_Al_lcao')
df.check_sum_rule(df1, df2)
t3 = time.time()
print 'For ground state calc, it took', (t2 - t1) / 60, 'minutes'
print 'For excited state calc, it took', (t3 - t2) / 60, 'minutes'
d = np.loadtxt('EELS_Al_lcao')
wpeak = 16.9 # eV
Nw = 169
if d[Nw, 1] > d[Nw-1, 1] and d[Nw, 2] > d[Nw+1, 2]:
pass
nbands=70, # The result should also be converged with respect to bands.
convergence={'bands':60}, # It's better NOT to converge all bands.
eigensolver='cg', # It's preferable to use 'cg' to calculate unoccupied states.
occupations=FermiDirac(0.05),
txt='out_gs.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('graphite.gpw','all')
# Part 2: Spectra calculations
f = paropen('graphite_q_list', 'w') # Write down q.
for i in range(1,8): # Loop over different q.
df = DF(calc='graphite.gpw',
nbands=60, # Use only bands that are converged in the gs calculation.
q=np.array([i/20., 0., 0.]), # Gamma - M excitation
#q=np.array([i/20., -i/20., 0.]) # Gamma - K excitation
w=np.linspace(0, 40, 401), # Spectra from 0-40 eV with 0.1 eV spacing.
eta=0.2, # Broadening parameter.
ecut=40+(i-1)*10, # In general, larger q requires larger planewave cutoff energy. #
txt='out_df_%d.txt' %(i)) # Write differnt output for different q.
df.get_EELS_spectrum(filename='graphite_EELS_%d' %(i)) # Use different filenames for different q
df.check_sum_rule() # Check f-sum rule.
print >> f, sqrt(np.inner(df.qq_v / Bohr, df.qq_v / Bohr))
nbands=nband+5,
parallel={'domain':1,
'band':1},
convergence={'bands':nband},
eigensolver = 'cg',
width=0.1)
atoms.set_calculator(calc)
atoms.get_potential_energy()
if EELS:
for i in range(1, 2):
w = np.linspace(0, 15, 301)
q = np.array([-i/64., i/64., 0.]) # Gamma - K
ecut = 40 + i*10
df = DF(calc=calc, q=q, w=w, eta=0.05, ecut = ecut,
txt='df_' + str(i) + '.out')
df.get_surface_response_function(z0=21.2/2, filename='be_EELS')
df.get_EELS_spectrum()
df.check_sum_rule()
df.write('df_' + str(i) + '.pckl')
if check:
d = np.loadtxt('be_EELS')
wpeak1 = 2.50 # eV
wpeak2 = 9.95
Nw1 = 50
Nw2 = 199
if (d[Nw1, 1] > d[Nw1-1, 1] and d[Nw1, 1] > d[Nw1+1, 1] and
d[Nw2, 1] > d[Nw2-1, 1] and d[Nw2, 1] > d[Nw2+1, 1]):
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(h=0.2, kpts=(4, 4, 4), occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C.gpw', 'all')
# Macroscopic dielectric constant calculation
q = np.array([0.0, 0.00001, 0.])
w = np.linspace(0, 24., 241)
df = DF(calc='C.gpw',
q=q,
w=(0., ),
eta=0.001,
ecut=50,
hilbert_trans=False,
optical_limit=True)
df1, df2 = df.get_dielectric_function()
eM1, eM2 = df.get_macroscopic_dielectric_constant(df1, df2)
eM1_ = 6.15185095143
eM2_ = 6.04815084635
if (np.abs(eM1 - eM1_) > 1e-5 or np.abs(eM2 - eM2_) > 1e-5):
print eM1, eM2
raise ValueError('Macroscopic dielectric constant not correct ! ')
# Absorption spectrum calculation
df = DF(calc='C.gpw',
def get_C6_coefficient(self,
ecut=100.,
nbands=None,
kcommsize=None,
gauss_legendre=None,
frequency_cut=None,
frequency_scale=None,
direction=2):
self.initialize_calculation(None,
ecut,
nbands,
kcommsize,
gauss_legendre,
frequency_cut,
frequency_scale)
d = direction
d_pro = []
for i in range(3):
if i != d:
d_pro.append(i)
dummy = DF(calc=self.calc,
eta=0.0,
w=self.w * 1j,
ecut=self.ecut,
hilbert_trans=False)
dummy.txt = devnull
dummy.initialize(simple_version=True)
npw = dummy.npw
del dummy
q = [0.,0.,0.]
q[d] = 1.e-5
if self.nbands is None:
nbands = npw
else:
nbands = self.nbands
if self.txt is sys.stdout:
txt = 'response.txt'
else:
txt='response_'+self.txt.name
df = DF(calc=self.calc,
xc=None,
nbands=nbands,
eta=0.0,
q=q,
txt=txt,
vcut=self.vcut,
w=self.w * 1j,
ecut=self.ecut,
comm=world,
optical_limit=True,
G_plus_q=True,
kcommsize=self.kcommsize,
hilbert_trans=False)
print >> self.txt, 'Calculating RPA response function'
print >> self.txt, 'Polarization: %s' % d
chi_wGG = df.get_chi(xc='RPA')
chi0_wGG = df.chi0_wGG
Nw_local = len(chi_wGG)
local_a0_w = np.zeros(Nw_local, dtype=complex)
a0_w = np.empty(len(self.w), complex)
local_a_w = np.zeros(Nw_local, dtype=complex)
a_w = np.empty(len(self.w), complex)
Gvec_Gv = np.dot(df.Gvec_Gc + np.array(q), df.bcell_cv)
gd = self.calc.density.gd
n_d = gd.get_size_of_global_array()[d]
d_d = gd.get_grid_spacings()[d]
r_d = np.array([i*d_d for i in range(n_d)])
print >> self.txt, 'Calculating real space integrals'
int_G = np.zeros(npw, complex)
for iG in range(npw):
if df.Gvec_Gc[iG, d_pro[0]] == 0 and df.Gvec_Gc[iG, d_pro[1]] == 0:
int_G[iG] = np.sum(r_d * np.exp(1j*Gvec_Gv[iG, d] * r_d))*d_d
int2_GG = np.outer(int_G, int_G.conj())
print >> self.txt, 'Calculating dynamic polarizability'
for i in range(Nw_local):
local_a0_w[i] = np.trace(np.dot(chi0_wGG[i], int2_GG))
local_a_w[i] = np.trace(np.dot(chi_wGG[i], int2_GG))
df.wcomm.all_gather(local_a0_w, a0_w)
df.wcomm.all_gather(local_a_w, a_w)
A = df.vol / gd.cell_cv[d,d]
a0_w *= A**2 / df.vol
a_w *= A**2 / df.vol
del df
C06 = np.sum(a0_w**2 * self.gauss_weights
* self.transform) * 3 / (2*np.pi)
C6 = np.sum(a_w**2 * self.gauss_weights
* self.transform) * 3 / (2*np.pi)
print >> self.txt, 'C06 = %s Ha*Bohr**6' % (C06.real / Ha)
print >> self.txt, 'C6 = %s Ha*Bohr**6' % (C6.real / Ha)
print >> self.txt
return C6.real / Ha, C06.real / Ha
h=0.15,
mode='lcao',
basis='dzp',
occupations=FermiDirac(0.01),
stencils=(3,3))
cluster.set_calculator(calc)
cluster.get_potential_energy()
calc.write('Au02.gpw','all')
if ABS:
df = DF(calc='Au02.gpw',
q=np.array([0.0, 0.0, 0.00001]),
w=np.linspace(0,14,141),
eta=0.1,
ecut=10,
optical_limit=True,
kcommsize=4)
df.get_absorption_spectrum()
d = np.loadtxt('Absorption.dat')
wpeak = 2.5 # eV
Nw = 25
if d[Nw, 4] > d[Nw-1, 4] and d[Nw, 4] > d[Nw+1, 4]:
pass
else:
raise ValueError('Plasmon peak not correct ! ')
if np.abs(d[Nw, 4] - 0.25788817927) > 5e-5:
import numpy as np
from ase.structure import bulk
from gpaw import GPAW
from gpaw.response.df import DF
# Part 1: Ground state calculation
atoms = bulk('Al', 'fcc',
a=4.043) # Generate fcc crystal structure for aluminum
calc = GPAW(h=0.2, kpts=(4, 4, 4)) # GPAW calculator initialization
atoms.set_calculator(calc)
atoms.get_potential_energy() # Ground state calculation is performed
calc.write('Al.gpw', 'all') # Use 'all' option to write wavefunctions
# Part 2: Spectrum calculation # DF: dielectric function object
df = DF(
calc='Al.gpw', # Ground state gpw file as input
q=np.array([
1. / 4., 0, 0
]), # Momentum transfer, must be the difference between two kpoints !
w=np.linspace(0, 24, 241)
) # The Energies (eV) for spectrum: from 0-24 eV with 0.1 eV spacing
df.get_EELS_spectrum() # By default, a file called 'EELS.dat' is generated
import numpy as np
from gpaw import GPAW
from gpaw.response.df import DF
w = np.linspace(0, 24., 481) # 0-24 eV with 0.05 eV spacing
q = np.array([0.0, 0.00001, 0.])
df = DF(calc='si.gpw',
q=q,
w=w,
eta=0.1, # Broadening parameter
ecut=150, # Energy cutoff for planewaves
optical_limit=True,
txt='df_2.out') # Output text
df1, df2 = df.get_dielectric_function()
df.get_absorption_spectrum(df1, df2, filename='si_abs.dat')
df.check_sum_rule(df1, df2)
df.write('df_2.pckl') # Save important parameters and data
nbands=nband + 5,
parallel={"domain": 1, "band": 1},
convergence={"bands": nband},
eigensolver="cg",
width=0.1,
)
atoms.set_calculator(calc)
atoms.get_potential_energy()
if EELS:
for i in range(1, 2):
w = np.linspace(0, 15, 301)
q = np.array([-i / 64.0, i / 64.0, 0.0]) # Gamma - K
ecut = 40 + i * 10
df = DF(calc=calc, q=q, w=w, eta=0.05, ecut=ecut, txt="df_" + str(i) + ".out")
df.get_surface_response_function(z0=21.2 / 2, filename="be_EELS")
df.get_EELS_spectrum()
df.check_sum_rule()
df.write("df_" + str(i) + ".pckl")
if check:
d = np.loadtxt("be_EELS")
wpeak1 = 2.50 # eV
wpeak2 = 9.95
Nw1 = 50
Nw2 = 199
if (
d[Nw1, 1] > d[Nw1 - 1, 1]
def get_E_q(self,
kcommsize=1,
index=None,
q=[0., 0., 0.],
integrated=True,
ecut=10,
nbands=None,
w=np.linspace(0, 200., 32),
extrapolate=True):
if index is None:
self.initialize_calculation(w, ecut, nbands, kcommsize,
extrapolate)
if abs(q[0]) < 0.001 and abs(q[1]) < 0.001 and abs(q[2]) < 0.001:
q = [1.e-5, 0., 0.]
optical_limit = True
else:
optical_limit = False
df = DF(calc=self.calc,
nbands=self.nbands,
eta=0.0,
q=q,
w=w * 1j,
ecut=ecut,
kcommsize=kcommsize,
optical_limit=optical_limit,
hilbert_trans=False)
df.txt = devnull
if index is None:
print >> self.txt, 'Calculating RPA dielectric matrix at:'
else:
print >> self.txt, '#', index, '- Calculating RPA dielectric matrix at:'
if optical_limit:
print >> self.txt, 'Q = [0 0 0]'
else:
print >> self.txt, 'Q = %s' % q
e_wGG = df.get_RPA_dielectric_matrix()
Nw_local = len(e_wGG)
local_E_q_w = np.zeros(Nw_local, dtype=complex)
E_q_w = np.empty(len(w), complex)
for i in range(Nw_local):
local_E_q_w[i] = (np.log(np.linalg.det(e_wGG[i])) + len(e_wGG[0]) -
np.trace(e_wGG[i]))
#local_E_q_w[i] = (np.sum(np.log(np.linalg.eigvals(e_wGG[i])))
# + self.npw - np.trace(e_wGG[i]))
df.wcomm.all_gather(local_E_q_w, E_q_w)
del df
del e_wGG
dw = w[1] - w[0]
E_q = dw * np.sum((E_q_w[:-1] + E_q_w[1:]) / 2.) / (2. * np.pi)
if extrapolate:
print
'''Fit tail to: Eq(w) = A**2/((w-B)**2 + C)**2'''
e1 = abs(E_q_w[-1])**0.5
e2 = abs(E_q_w[-2])**0.5
e3 = abs(E_q_w[-3])**0.5
w1 = w[-1]
w2 = w[-2]
w3 = w[-3]
B = (((e3 * w3**2 - e1 * w1**2) / (e1 - e3) -
(e2 * w2**2 - e1 * w1**2) / (e1 - e2)) /
((2 * w3 * e3 - 2 * w1 * e1) / (e1 - e3) -
(2 * w2 * e2 - 2 * w1 * e1) / (e1 - e2)))
C = ((w2 - B)**2 * e2 - (w1 - B)**2 * e1) / (e1 - e2)
A = e1 * ((w1 - B)**2 + C)
if C > 0:
E_q -= A**2 * (np.pi / (4 * C**1.5) - (w1 - B) /
((w1 - B)**2 + C) / (2 * C) - np.arctan(
(w1 - B) / C**0.5) /
(2 * C**1.5)) / (2 * np.pi)
else:
E_q += A**2 * ((w1 - B) / ((w1 - B)**2 + C) / (2 * C) + np.log(
(w1 - B - abs(C)**0.5) / (w1 - B + abs(C)**0.5)) /
(4 * C * abs(C)**0.5)) / (2 * np.pi)
print >> self.txt, 'E_c(Q) = %s eV' % E_q.real
print >> self.txt
if index is None:
print >> self.txt, 'Calculation completed at: ', ctime()
print >> self.txt
print >> self.txt, '------------------------------------------------------'
if integrated:
return E_q
else:
return E_q_w
atoms.center()
calc = GPAW(gpts=(12,12,12),
eigensolver=RMM_DIIS(),
mixer=Mixer(0.1,3),
kpts=(4,4,4),
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al1.gpw','all')
# Excited state calculation
q = np.array([1./4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al1.gpw', q=q, w=w, eta=0.2, ecut=50)
#df.write('Al.pckl')
df.get_EELS_spectrum(filename='EELS_Al_1')
atoms = Atoms('Al8',scaled_positions=[(0,0,0),
(0.5,0,0),
(0,0.5,0),
(0,0,0.5),
(0.5,0.5,0),
(0.5,0,0.5),
(0.,0.5,0.5),
(0.5,0.5,0.5)],
cell=[(0,a,a),(a,0,a),(a,a,0)],
pbc=True)
calc = GPAW(gpts=(24,24,24),
def get_E_q(self,
kcommsize=1,
index=None,
q=[0., 0., 0.],
integrated=True,
ecut=10,
nbands=None,
w=np.linspace(0, 200., 32),
extrapolate=True):
if index is None:
self.initialize_calculation(w, ecut, nbands, kcommsize, extrapolate)
if abs(q[0]) < 0.001 and abs(q[1]) < 0.001 and abs(q[2]) < 0.001:
q = [1.e-5, 0., 0.]
optical_limit = True
else:
optical_limit = False
df = DF(calc=self.calc,
nbands=self.nbands,
eta=0.0,
q=q,
w=w * 1j,
ecut=ecut,
kcommsize=kcommsize,
optical_limit=optical_limit,
hilbert_trans=False)
df.txt = devnull
if index is None:
print >> self.txt, 'Calculating RPA dielectric matrix at:'
else:
print >> self.txt, '#', index, '- Calculating RPA dielectric matrix at:'
if optical_limit:
print >> self.txt, 'Q = [0 0 0]'
else:
print >> self.txt, 'Q = %s' % q
e_wGG = df.get_RPA_dielectric_matrix()
Nw_local = len(e_wGG)
local_E_q_w = np.zeros(Nw_local, dtype=complex)
E_q_w = np.empty(len(w), complex)
for i in range(Nw_local):
local_E_q_w[i] = (np.log(np.linalg.det(e_wGG[i]))
+ len(e_wGG[0]) - np.trace(e_wGG[i]))
#local_E_q_w[i] = (np.sum(np.log(np.linalg.eigvals(e_wGG[i])))
# + self.npw - np.trace(e_wGG[i]))
df.wcomm.all_gather(local_E_q_w, E_q_w)
del df
del e_wGG
dw = w[1] - w[0]
E_q = dw * np.sum((E_q_w[:-1] + E_q_w[1:])/2.) / (2.*np.pi)
if extrapolate:
print
'''Fit tail to: Eq(w) = A**2/((w-B)**2 + C)**2'''
e1 = abs(E_q_w[-1])**0.5
e2 = abs(E_q_w[-2])**0.5
e3 = abs(E_q_w[-3])**0.5
w1 = w[-1]
w2 = w[-2]
w3 = w[-3]
B = (((e3*w3**2-e1*w1**2)/(e1-e3) - (e2*w2**2-e1*w1**2)/(e1-e2))
/ ((2*w3*e3-2*w1*e1)/(e1-e3) - (2*w2*e2-2*w1*e1)/(e1-e2)))
C = ((w2-B)**2*e2 - (w1-B)**2*e1)/(e1-e2)
A = e1*((w1-B)**2+C)
if C > 0:
E_q -= A**2*(np.pi/(4*C**1.5)
- (w1-B)/((w1-B)**2+C)/(2*C)
- np.arctan((w1-B)/C**0.5)/(2*C**1.5)) / (2*np.pi)
else:
E_q += A**2*((w1-B)/((w1-B)**2+C)/(2*C)
+ np.log((w1-B-abs(C)**0.5)/(w1-B+abs(C)**0.5))
/(4*C*abs(C)**0.5)) / (2*np.pi)
print >> self.txt, 'E_c(Q) = %s eV' % E_q.real
print >> self.txt
if index is None:
print >> self.txt, 'Calculation completed at: ', ctime()
print >> self.txt
print >> self.txt, '------------------------------------------------------'
if integrated:
return E_q
else:
return E_q_w
basis='dzp',
xc='LDA')
atoms.set_calculator(calc)
t1 = time.time()
atoms.get_potential_energy()
t2 = time.time()
calc.write('Al.gpw','all')
t3 = time.time()
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al.gpw', q=q, w=w, eta=0.2, ecut=50)
#df.write('Al.pckl')
df.get_EELS_spectrum(filename='EELS_Al_lcao')
df.check_sum_rule()
t4 = time.time()
print 'For ground state calc, it took', (t2 - t1) / 60, 'minutes'
print 'For writing gpw, it took', (t3 - t2) / 60, 'minutes'
print 'For excited state calc, it took', (t4 - t3) / 60, 'minutes'
d = np.loadtxt('EELS_Al_lcao')
wpeak = 16.9 # eV
Nw = 169
if d[Nw, 1] > d[Nw-1, 1] and d[Nw, 2] > d[Nw+1, 2]:
pass
'domain': 1,
'band': 1
},
idiotproof=False, # allow uneven distribution of k-points
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
#calc.write('Al.gpw','all')
t2 = time.time()
# Excited state calculation
q = np.array([1 / 4., 0., 0.])
w = np.linspace(0, 24, 241)
df = DF(calc=calc, q=q, w=w, eta=0.2, ecut=50)
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2, filename='EELS_Al')
df.check_sum_rule()
t3 = time.time()
print 'For ground state calc, it took', (t2 - t1) / 60, 'minutes'
print 'For excited state calc, it took', (t3 - t2) / 60, 'minutes'
d = np.loadtxt('EELS_Al')
wpeak = 15.7 # eV
Nw = 157
if d[Nw, 1] > d[Nw - 1, 1] and d[Nw, 2] > d[Nw + 1, 2]:
pass
else:
def screened_interaction_kernel(self, iq):
"""Calcuate W_GG(w) for a given q.
if static: return W_GG(w=0)
is not static: return W_GG(q,w) - Vc_GG
"""
q = self.ibzq_qc[iq]
w = self.w_w.copy()*Hartree
optical_limit = False
if np.abs(q).sum() < 1e-8:
q = np.array([1e-12, 0, 0]) # arbitrary q, not really need to be calculated
optical_limit = True
hilbert_trans = True
if self.ppa or self.static:
hilbert_trans = False
df = DF(calc=self.calc, q=q.copy(), w=w, nbands=self.nbands, eshift=None,
optical_limit=optical_limit, hilbert_trans=hilbert_trans, xc='RPA', time_ordered=True,
rpad=self.rpad, vcut=self.vcut, G_plus_q=True,
eta=self.eta*Hartree, ecut=self.ecut.copy()*Hartree,
txt='df.out', comm=self.dfcomm, kcommsize=self.kcommsize)
df.initialize()
df.e_skn = self.e_skn.copy()
df.calculate()
dfinv_wGG = df.get_inverse_dielectric_matrix(xc='RPA')
assert df.ecut[0] == self.ecut[0]
if not self.static and not self.ppa:
assert df.eta == self.eta
assert df.Nw == self.Nw
assert df.dw == self.dw
# calculate Coulomb kernel and use truncation in 2D
delta_GG = np.eye(df.npw)
Vq_G = np.diag(calculate_Kc(q,
df.Gvec_Gc,
self.acell_cv,
self.bcell_cv,
self.pbc,
integrate_gamma=True,
N_k=self.kd.N_c,
vcut=self.vcut))**0.5
if (self.vcut == '2D' and df.optical_limit) or self.numint:
for iG in range(len(df.Gvec_Gc)):
if df.Gvec_Gc[iG, 0] == 0 and df.Gvec_Gc[iG, 1] == 0:
v_q, v0_q = calculate_Kc_q(self.acell_cv,
self.bcell_cv,
self.pbc,
self.kd.N_c,
vcut=self.vcut,
q_qc=np.array([q]),
Gvec_c=df.Gvec_Gc[iG])
Vq_G[iG] = v_q[0]**0.5
self.Kc_GG = np.outer(Vq_G, Vq_G)
if self.ppa:
dfinv1_GG = dfinv_wGG[0] - delta_GG
dfinv2_GG = dfinv_wGG[1] - delta_GG
self.wt_GG = self.E0 * np.sqrt(dfinv2_GG / (dfinv1_GG - dfinv2_GG))
self.R_GG = - self.wt_GG / 2 * dfinv1_GG
del dfinv_wGG
dfinv_wGG = np.array([1j*pi*self.R_GG + delta_GG])
if self.static:
assert len(dfinv_wGG) == 1
W_GG = dfinv_wGG[0] * self.Kc_GG
return df, W_GG
else:
Nw = np.shape(dfinv_wGG)[0]
W_wGG = np.zeros_like(dfinv_wGG)
for iw in range(Nw):
dfinv_wGG[iw] -= delta_GG
W_wGG[iw] = dfinv_wGG[iw] * self.Kc_GG
return df, W_wGG
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C_kpt8.gpw','all')
if bse:
bse = BSE('C_kpt8.gpw',w=np.linspace(0,20,201),
q=np.array([0,0,0.5]),optical_limit=True,ecut=50.,
nbands=8)
bse.get_dielectric_function('C_bse.dat')
if df:
from gpaw.response.df import DF
df = DF('C_kpt8.gpw',w=np.linspace(0,20,201),q=np.array([0,0,0.5]),
optical_limit=True,ecut=50., hilbert_trans=False)
df.get_absorption_spectrum(filename='C.dat')
if check_spectrum:
d = np.loadtxt('C_bse.dat')[:,2]
Nw1 = 97
Nw2 = 109
if d[Nw1] > d[Nw1-1] and d[Nw1] > d[Nw1+1] and \
d[Nw2] > d[Nw2-1] and d[Nw2] > d[Nw2+1] :
pass
else:
raise ValueError('Absorption peak not correct ! ')
if np.abs(d[Nw1] - 68.8295454438) > 1e-5 or \
import numpy as np
from gpaw import GPAW
from gpaw.response.df import DF
w = np.linspace(0, 24., 481) # 0-24 eV with 0.05 eV spacing
q = np.array([0.0, 0.00001, 0.])
df = DF(calc='si.gpw',
q=q,
w=w,
eta=0.1, # Broadening parameter
ecut=150, # Energy cutoff for planewaves
optical_limit=True,
txt='df_2.out') # Output text
df.get_absorption_spectrum(filename='si_abs.dat')
df.check_sum_rule()
df.write('df_2.pckl') # Save important parameters and data
calc.write('Al.gpw','all')
if bse:
bse = BSE('Al.gpw',w=np.linspace(0,24,241),
q=np.array([0.25, 0, 0]),ecut=50., eta=0.2)
bse.get_dielectric_function('Al_bse.dat')
if df:
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al.gpw', q=q, w=w, eta=0.2, ecut=50,hilbert_trans=False)
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2,filename='Al_df.dat')
df.write('Al.pckl')
df.check_sum_rule()
if check_spectrum:
d = np.loadtxt('Al_bse.dat')[:,2]
wpeak = 16.4
Nw = 164
if d[Nw] > d[Nw-1] and d[Nw] > d[Nw+1]:
pass
else:
raise ValueError('Plasmon peak not correct ! ')
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(h=0.2,
kpts=(4,4,4),
occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C.gpw','all')
# Macroscopic dielectric constant calculation
q = np.array([0.0, 0.00001, 0.])
w = np.linspace(0, 24., 241)
df = DF(calc='C.gpw', q=q, w=(0.,), eta=0.001,
ecut=50, hilbert_trans=False, optical_limit=True)
df1, df2 = df.get_dielectric_function()
eM1, eM2 = df.get_macroscopic_dielectric_constant(df1, df2)
eM1_ = 6.15185095143
eM2_ = 6.04815084635
if (np.abs(eM1 - eM1_) > 1e-5 or
np.abs(eM2 - eM2_) > 1e-5):
print eM1, eM2
raise ValueError('Macroscopic dielectric constant not correct ! ')
# Absorption spectrum calculation
df = DF(calc='C.gpw', q=q, w=w, eta=0.25,
ecut=50, optical_limit=True, txt='C_df.out')
def initialize_calculation(self,
w,
ecut,
nbands,
kcommsize,
gauss_legendre,
frequency_cut,
frequency_scale):
if kcommsize is None:
if len(self.calc.wfs.bzk_kc) == 1:
kcommsize = 1
else:
kcommsize = world.size
if w is not None:
assert (gauss_legendre is None and
frequency_cut is None and
frequency_scale is None)
else:
if gauss_legendre is None:
gauss_legendre = 16
self.gauss_points, self.gauss_weights = p_roots(gauss_legendre)
if frequency_scale is None:
frequency_scale = 2.0
if frequency_cut is None:
frequency_cut = 800.
ys = 0.5 - 0.5 * self.gauss_points
ys = ys[::-1]
w = (-np.log(1-ys))**frequency_scale
w *= frequency_cut/w[-1]
alpha = (-np.log(1-ys[-1]))**frequency_scale/frequency_cut
transform = (-np.log(1-ys))**(frequency_scale-1) \
/ (1-ys)*frequency_scale/alpha
self.transform = transform
dummy = DF(calc=self.calc,
eta=0.0,
w=w * 1j,
q=[0.,0.,0.0001],
ecut=ecut,
optical_limit=True,
hilbert_trans=False,
kcommsize=kcommsize)
dummy.txt = devnull
dummy.initialize(simple_version=True)
self.npw = dummy.npw
self.ecut = ecut
self.w = w
self.gauss_legendre = gauss_legendre
self.frequency_cut = frequency_cut
self.frequency_scale = frequency_scale
self.kcommsize = kcommsize
self.nbands = nbands
print >> self.txt
print >> self.txt, 'Planewave cutoff : %s eV' % ecut
print >> self.txt, 'Number of Planewaves at Gamma : %s' % self.npw
if self.nbands is None:
print >> self.txt, 'Response function bands :'\
+ ' Equal to number of Planewaves'
else:
print >> self.txt, 'Response function bands : %s' \
% self.nbands
print >> self.txt, 'Frequencies'
if self.gauss_legendre is not None:
print >> self.txt, ' Gauss-Legendre integration '\
+ 'with %s frequency points' % len(self.w)
print >> self.txt, ' Frequency cutoff is '\
+ '%s eV and scale (B) is %s' % (self.w[-1],
self.frequency_scale)
else:
print >> self.txt, ' %s specified frequency points' \
% len(self.w)
print >> self.txt, ' Frequency cutoff is %s eV' \
% self.w[-1]
print >> self.txt
print >> self.txt, 'Parallelization scheme'
print >> self.txt, ' Total CPUs : %d' % dummy.comm.size
if dummy.kd.nbzkpts == 1:
print >> self.txt, ' Band parsize : %d' % dummy.kcomm.size
else:
print >> self.txt, ' Kpoint parsize : %d' % dummy.kcomm.size
print >> self.txt, ' Frequency parsize : %d' % dummy.wScomm.size
print >> self.txt, 'Memory usage estimate'
print >> self.txt, ' chi0_wGG(Q) : %f M / cpu' \
% (dummy.Nw_local * self.npw**2 * 16. / 1024**2)
print >> self.txt
del dummy
import numpy as np
from ase.structure import bulk
from gpaw import GPAW
from gpaw.response.df import DF
# Part 1: Ground state calculation
atoms = bulk('Si', 'diamond', a=5.431) # Generate diamond crystal structure for silicon
calc = GPAW(h=0.20, kpts=(4,4,4)) # GPAW calculator initialization
atoms.set_calculator(calc)
atoms.get_potential_energy() # Ground state calculation is performed
calc.write('si.gpw','all') # Use 'all' option to write wavefunction
# Part 2 : Spectrum calculation # DF: dielectric function object
df = DF(calc='si.gpw', # Ground state gpw file (with wavefunction) as input
q=np.array([0.0, 0.00001, 0.0]), # Momentum transfer, here excites in y-direction
w=np.linspace(0,14,141), # The Energies (eV) for spectrum: from 0-14 eV with 0.1 eV spacing
optical_limit=True) # Indicates that its a optical spectrum calculation
df.get_absorption_spectrum() # By default, a file called 'Absorption.dat' is generated
convergence={'bands':70})
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('si.gpw','all')
if ABS:
w = np.linspace(0, 24, 481)
q = np.array([0.0, 0.00001, 0.])
# getting macroscopic constant
df = DF(calc='si.gpw',
q=q,
w=(0.,),
eta=0.001,
hilbert_trans=False,
ecut=150,
optical_limit=True,
txt='df_1.out')
eM1, eM2 = df.get_macroscopic_dielectric_constant()
df.write('df_1.pckl')
if np.abs(eM1 - 13.991793) > 1e-3 or np.abs(eM2 - 12.589129) > 1e-3:
print eM1, eM2
raise ValueError('Please check dielectric constant !')
#getting absorption spectrum
df = DF(calc='si.gpw',
q=q,
a = 4.043
atoms = bulk('Al', 'fcc', a=a)
atoms.center()
calc = GPAW(gpts=(12,12,12),
kpts=(4,4,4),
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al1.gpw','all')
# Excited state calculation
q = np.array([1./4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al1.gpw', q=q, w=w, eta=0.2, ecut=50)
df1, df2 = df.get_dielectric_function()
#df.write('Al.pckl')
df.get_EELS_spectrum(df1, df2,filename='EELS_Al_1')
atoms = Atoms('Al8',scaled_positions=[(0,0,0),
(0.5,0,0),
(0,0.5,0),
(0,0,0.5),
(0.5,0.5,0),
(0.5,0,0.5),
(0.,0.5,0.5),
(0.5,0.5,0.5)],
cell=[(0,a,a),(a,0,a),(a,a,0)],
pbc=True)
from gpaw.response.df import DielectricFunction as DF
df = DF(
'LiF_fulldiag.gpw',
domega0=0.01, # grid-spacing at 0 eV
omega2=10.0, # frequency where grid-spacing has doubled to 0.02 eV
eta=0.1, # broadening parameter
nbands=60, # number of bands to consider for building chi
ecut=30, # energy cutoff for planewaves
txt='LiF_RPA_out2.txt')
# Calculate the dielectric function without and with local field effects:
df.get_dielectric_function()
bse = BSE('Al.gpw',
w=np.linspace(0, 24, 241),
q=np.array([0.25, 0, 0]),
ecut=50.,
eta=0.2)
bse.get_dielectric_function('Al_bse.dat')
if df:
# Excited state calculation
q = np.array([1 / 4., 0., 0.])
w = np.linspace(0, 24, 241)
df = DF(calc='Al.gpw', q=q, w=w, eta=0.2, ecut=50, hilbert_trans=False)
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2, filename='Al_df.dat')
df.write('Al.pckl')
df.check_sum_rule()
if check_spectrum:
d = np.loadtxt('Al_bse.dat')[:, 2]
wpeak = 16.4
Nw = 164
if d[Nw] > d[Nw - 1] and d[Nw] > d[Nw + 1]:
pass
else:
raise ValueError('Plasmon peak not correct ! ')
import numpy as np
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.response.df import DF
# Part 1: Ground state calculation
atoms = bulk('Si', 'diamond', a=5.431) # Generate diamond crystal structure for silicon
calc = GPAW(h=0.20, kpts=(4,4,4)) # GPAW calculator initialization
atoms.set_calculator(calc)
atoms.get_potential_energy() # Ground state calculation is performed
calc.write('si.gpw','all') # Use 'all' option to write wavefunction
# Part 2 : Spectrum calculation # DF: dielectric function object
df = DF(calc='si.gpw', # Ground state gpw file (with wavefunction) as input
q=np.array([0.0, 0.00001, 0.0]), # Momentum transfer, here excites in y-direction
w=np.linspace(0,14,141), # The Energies (eV) for spectrum: from 0-14 eV with 0.1 eV spacing
optical_limit=True) # Indicates that its a optical spectrum calculation
df.get_absorption_spectrum() # By default, a file called 'Absorption.dat' is generated
# view(atoms)
atoms.get_potential_energy()
calc.write('graphite.gpw','all')
if EELS:
f = paropen('graphite_q_list', 'w')
for i in range(1,8):
w = np.linspace(0, 40, 401)
q = np.array([i/20., 0., 0.]) # Gamma-M excitation
#q = np.array([i/20., -i/20., 0.]) # Gamma-K excitation
ecut = 40 + (i-1)*10
df = DF(calc='graphite.gpw', nbands=nband, q=q, w=w,
eta=0.2,ecut=ecut)
df.get_EELS_spectrum(filename='graphite_EELS_' + str(i))
df.check_sum_rule()
print >> f, sqrt(np.inner(df.qq_v / Bohr, df.qq_v / Bohr)), ecut
if rank == 0:
os.remove('graphite.gpw')
import numpy as np
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.response.df import DF
# Part 1: Ground state calculation
atoms = bulk('Al', 'fcc', a=4.043) # Generate fcc crystal structure for aluminum
calc = GPAW(h=0.2, kpts=(4,4,4)) # GPAW calculator initialization
atoms.set_calculator(calc)
atoms.get_potential_energy() # Ground state calculation is performed
calc.write('Al.gpw','all') # Use 'all' option to write wavefunctions
# Part 2: Spectrum calculation # DF: dielectric function object
df = DF(calc='Al.gpw', # Ground state gpw file as input
q=np.array([1./4., 0, 0]), # Momentum transfer, must be the difference between two kpoints !
w=np.linspace(0, 24, 241)) # The Energies (eV) for spectrum: from 0-24 eV with 0.1 eV spacing
df.get_EELS_spectrum() # By default, a file called 'EELS.dat' is generated
atoms.get_potential_energy()
calc.write('graphite.gpw','all')
if EELS:
f = paropen('graphite_q_list', 'w')
for i in range(1,8):
w = np.linspace(0, 40, 401)
q = np.array([i/20., 0., 0.]) # Gamma-M excitation
#q = np.array([i/20., -i/20., 0.]) # Gamma-K excitation
ecut = 40 + (i-1)*10
df = DF(calc='graphite.gpw', nbands=nband, q=q, w=w,
eta=0.2,ecut=ecut)
df1, df2 = df.get_dielectric_function()
df.get_EELS_spectrum(df1, df2,filename='graphite_EELS_' + str(i))
df.check_sum_rule(df1, df2)
print >> f, sqrt(np.inner(df.qq_v / Bohr, df.qq_v / Bohr)), ecut
if rank == 0:
os.remove('graphite.gpw')
eigensolver='cg',
occupations=FermiDirac(0.001),
convergence={'bands':70})
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('si.gpw','all')
if ABS:
w = np.linspace(0, 24, 481)
q = np.array([0.0, 0.00001, 0.])
# getting macroscopic constant
df = DF(calc='si.gpw', q=q, w=(0.,), eta=0.0001,
hilbert_trans=False, txt='df_1.out',
ecut=150, optical_limit=True)
df1, df2 = df.get_dielectric_function()
eM1, eM2 = df.get_macroscopic_dielectric_constant(df1, df2)
df.write('df_1.pckl')
if np.abs(eM1 - 13.992277) > 1e-4 or np.abs(eM2 - 12.589596) > 1e-4:
print eM1, eM2
raise ValueError('Pls check dielectric constant !')
#getting absorption spectrum
df = DF(calc='si.gpw', q=q, w=w, eta=0.1,
ecut=150, optical_limit=True, txt='df_2.out')
calc = GPAW(mode='pw', kpts=kpts, basis='dzp', dtype=complex,
maxiter=500,
usesymm=None, communicator=serial_comm)
atoms.set_calculator(calc)
atoms.get_potential_energy()
gd = GridDescriptor(calc.wfs.gd.N_c, calc.atoms.cell / Bohr,
pbc_c=True, comm=serial_comm)
kd = calc.wfs.kd
setups = calc.wfs.setups
bzk_kc = calc.wfs.kd.bzk_kc
spos_ac = calc.atoms.get_scaled_positions()
nbands = calc.get_number_of_bands()
nspins = calc.wfs.nspins
df = DF(calc)
df.spos_ac = spos_ac
if mode == 'fd':
pt = LFC(gd, [setup.pt_j for setup in setups],
KPointDescriptor(bzk_kc),
dtype=calc.wfs.dtype)
pt.set_positions(spos_ac)
for spin in range(nspins):
for k in range(len(bzk_kc)):
ibzk = k # since no symmetry
u = kd.get_rank_and_index(spin, ibzk)[1]
kpt = calc.wfs.kpt_u[u]
for n in range(nbands):
P_ai = pt.dict()