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)
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 ! ')
if np.abs(d[Nw] - 27.5317730322) > 1e-5:
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))
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 ! ')
if np.abs(d[Nw] - 27.4958893542) > 1e-5:
print d[Nw]
},
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:
raise ValueError('Plasmon peak not correct ! ')
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')
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 ! ')
if np.abs(d[Nw] - 27.5317730322) > 1e-5:
print d[Nw]
kpts=(4,4,4),
parallel={'domain':1,
'band':1},
idiotproof=False, # allow uneven distribution of k-points
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
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=(50,50,50))
df.get_EELS_spectrum(filename='EELS_Al')
df.check_sum_rule()
df.write('Al.pckl')
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:
raise ValueError('Plasmon peak not correct ! ')
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
else:
raise ValueError('Plasmon peak not correct ! ')
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),
eigensolver=RMM_DIIS(),
mixer=Mixer(0.1,3),
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]
and d[Nw1, 1] > d[Nw1 + 1, 1]
and d[Nw2, 1] > d[Nw2 - 1, 1]
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
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
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('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
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)
calc = GPAW(gpts=(24,24,24),
kpts=(2,2,2),
xc='LDA')
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))
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]):
pass
else:
