def check_df(name, ref_energy, ref_loss, ref_energy_lfe, ref_loss_lfe, **kwargs_override):
kwargs = dict(calc=calc, frequencies=w.copy(), eta=0.5, ecut=30, txt="df.%s.txt" % name)
kwargs.update(kwargs_override)
df = DielectricFunction(**kwargs)
fname = "dfdump.%s.dat" % name
df.get_eels_spectrum("RPA", q_c=q, filename=fname)
world.barrier()
d = np.loadtxt(fname, delimiter=",")
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 get_hydrogen_chain_dielectric_function(NH, NK):
a = Atoms('H', cell=[1, 1, 1], pbc=True)
a.center()
a = a.repeat((1, 1, NH))
a.calc = GPAW(mode=PW(200), kpts={'size': (1, 1, NK), 'gamma': True},
parallel={'band': 1}, dtype=complex, gpts=(10, 10, 10 * NH))
a.get_potential_energy()
a.calc.diagonalize_full_hamiltonian(nbands=2 * NH)
a.calc.write('H_chain.gpw', 'all')
DF = DielectricFunction('H_chain.gpw', ecut=1e-3, hilbert=False,
omega2=np.inf, intraband=False)
eps_NLF, eps_LF = DF.get_dielectric_function(direction='z')
omega_w = DF.get_frequencies()
return omega_w, eps_LF
calc = GPAW(mode=PW(200),
kpts=(4,4,4),
parallel={'band':1},
idiotproof=False, # allow uneven distribution of k-points
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al', 'all')
t2 = time.time()
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DielectricFunction(calc='Al', frequencies=w, eta=0.2, ecut=50,
hilbert=False)
df.get_eels_spectrum(xc='RPA', filename='EELS_Al', q_c=q)
#df.check_sum_rule()
#df.write('Al.pckl')
t3 = time.time()
print ''
print 'For ground state calc, it took', (t2 - t1) / 60, 'minutes'
print 'For excited state calc, it took', (t3 - t2) / 60, 'minutes'
world.barrier()
d = np.loadtxt('EELS_Al',delimiter=',')
# New results are compared with test values
wpeak1,Ipeak1 = findpeak(d[:,0],d[:,1])
atoms.get_potential_energy()
calc.set(kpts=(20, 20, 7), fixdensity=True)
atoms.get_potential_energy()
# The result should also be converged with respect to bands:
calc.diagonalize_full_hamiltonian(nbands=60)
calc.write('graphite.gpw', 'all')
# Part 2: Spectra calculations
f = paropen('graphite_q_list', 'w') # write q
for i in range(1, 6): # loop over different q
df = DielectricFunction(calc='graphite.gpw',
domega0=0.01,
eta=0.2, # Broadening parameter.
ecut=100,
# write different output for different q:
txt='out_df_%d.txt' % i)
q_c = [i / 20.0, 0.0, 0.0] # Gamma - M excitation
df.get_eels_spectrum(q_c=q_c, filename='graphite_EELS_%d' % i)
# Calculate cartesian momentum vector:
cell_cv = atoms.get_cell()
bcell_cv = 2 * np.pi * np.linalg.inv(cell_cv).T
q_v = np.dot(q_c, bcell_cv)
print(sqrt(np.inner(q_v, q_v)), file=f)
f.close()
from gpaw.test import equal, findpeak
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(mode='pw',
kpts=(3, 3, 3),
eigensolver='rmm-diis',
occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C.gpw', 'all')
# Macroscopic dielectric constant calculation
df = DielectricFunction('C.gpw', frequencies=(0.,), eta=0.001, ecut=200,
hilbert=False)
eM1, eM2 = df.get_macroscopic_dielectric_constant()
eM1_ = 9.725
eM2_ = 9.068
equal(eM1, eM1_, 0.01)
equal(eM2, eM2_, 0.01)
# Absorption spectrum calculation
df = DielectricFunction('C.gpw', eta=0.25, ecut=200,
frequencies=np.linspace(0, 24., 241), hilbert=False)
b0, b = df.get_dielectric_function(filename=None)
df.check_sum_rule(b.imag)
equal(b0[0].real, eM1_, 0.01)
xc='LDA',
occupations=FermiDirac(0.001)) # Use small FD smearing
atoms.set_calculator(calc)
atoms.get_potential_energy() # Get ground state density
# Restart Calculation with fixed density and dense kpoint sampling
calc.set(kpts={'density': 15.0, 'gamma': False}, # Dense kpoint sampling
fixdensity=True)
atoms.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=70) # Diagonalize Hamiltonian
calc.write('si_large.gpw', 'all') # Write wavefunctions
# Getting absorption spectrum
df = DielectricFunction(calc='si_large.gpw',
eta=0.05,
domega0=0.02,
ecut=150)
df.get_dielectric_function(filename='si_abs.csv')
# Getting macroscopic constant
df = DielectricFunction(calc='si_large.gpw',
frequencies=[0.0],
hilbert=False,
eta=0.0001,
ecut=150,
)
epsNLF, epsLF = df.get_macroscopic_dielectric_constant()
# Make table
epsrefNLF = 14.08 # From [1] in top
eigensolver=RMM_DIIS(),
mixer=Mixer(0.1,3),
kpts=(4,4,4),
parallel={'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 = DielectricFunction(calc=calc, frequencies=w, eta=0.2, ecut=50)
eels_NLFC_w, eels_LFC_w = df.get_eels_spectrum(filename='EELS_Al', q_c=q)
df_NLFC_w, df_LFC_w = df.get_dielectric_function(q_c=q)
df.check_sum_rule(spectrum=np.imag(df_NLFC_w))
df.check_sum_rule(spectrum=np.imag(df_LFC_w))
df.check_sum_rule(spectrum=eels_NLFC_w)
df.check_sum_rule(spectrum=eels_LFC_w)
#df.write('Al.pckl')
t3 = time.time()
print('')
print('For ground state calc, it took', (t2 - t1) / 60, 'minutes')
txt='large.txt')
a1.get_potential_energy()
a2.get_potential_energy()
# Use twice as many bands for expanded structure
a1.calc.diagonalize_full_hamiltonian(nbands=20)
a2.calc.diagonalize_full_hamiltonian(nbands=40)
a1.calc.write('gs_Na_small.gpw', 'all')
a2.calc.write('gs_Na_large.gpw', 'all')
# Calculate the dielectric functions
df1 = DielectricFunction('gs_Na_small.gpw',
omegamax=15,
domega0=0.05,
hilbert=True,
ecut=150)
df1NLFCx, df1LFCx = df1.get_dielectric_function(direction='x')
df1NLFCy, df1LFCy = df1.get_dielectric_function(direction='y')
df1NLFCz, df1LFCz = df1.get_dielectric_function(direction='z')
df2 = DielectricFunction('gs_Na_large.gpw',
omegamax=15,
domega0=0.05,
hilbert=True,
ecut=150)
df2NLFCx, df2LFCx = df2.get_dielectric_function(direction='x')
df2NLFCy, df2LFCy = df2.get_dielectric_function(direction='y')
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()
calc = GPAW(mode=PW(200),
kpts=(4,4,4),
parallel={'band':1},
idiotproof=False, # allow uneven distribution of k-points
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al', 'all')
t2 = time.time()
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DielectricFunction(calc='Al', frequencies=w, eta=0.2, ecut=50,
hilbert=False)
df.get_eels_spectrum(xc='RPA', filename='EELS_Al', q_c=q)
#df.check_sum_rule()
#df.write('Al.pckl')
t3 = time.time()
print('')
print('For ground state calc, it took', (t2 - t1) / 60, 'minutes')
print('For excited state calc, it took', (t3 - t2) / 60, 'minutes')
world.barrier()
d = np.loadtxt('EELS_Al',delimiter=',')
# New results are compared with test values
wpeak1,Ipeak1 = findpeak(d[:,0],d[:,1])
cell=(a, a, a),
pbc=True)
a1.calc = GPAW(gpts=(10, 10, 10),
mode=PW(300),
kpts={'size': (10, 10, 10), 'gamma': True},
parallel={'band': 1},
txt='small.txt')
a1.get_potential_energy()
a1.calc.diagonalize_full_hamiltonian(nbands=20)
a1.calc.write('gs_Na.gpw', 'all')
# Calculate the dielectric functions
df1 = DielectricFunction('gs_Na.gpw',
nblocks=1,
ecut=400,
txt='1block.txt')
df1NLFCx, df1LFCx = df1.get_dielectric_function(direction='x')
df1NLFCy, df1LFCy = df1.get_dielectric_function(direction='y')
df1NLFCz, df1LFCz = df1.get_dielectric_function(direction='z')
df2 = DielectricFunction('gs_Na.gpw',
nblocks=2,
ecut=400,
txt='2block.txt')
df2NLFCx, df2LFCx = df2.get_dielectric_function(direction='x')
df2NLFCy, df2LFCy = df2.get_dielectric_function(direction='y')
df2NLFCz, df2LFCz = df2.get_dielectric_function(direction='z')
from gpaw.test import equal, findpeak
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(mode='pw',
kpts=(3, 3, 3),
eigensolver='rmm-diis',
occupations=FermiDirac(0.001))
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('C.gpw', 'all')
# Macroscopic dielectric constant calculation
df = DielectricFunction('C.gpw', frequencies=(0.,), eta=0.001, ecut=200,
hilbert=False)
eM1, eM2 = df.get_macroscopic_dielectric_constant()
eM1_ = 9.725
eM2_ = 9.068
equal(eM1, eM1_, 0.01)
equal(eM2, eM2_, 0.01)
# Absorption spectrum calculation
df = DielectricFunction('C.gpw', eta=0.25, ecut=200,
frequencies=np.linspace(0, 24., 241), hilbert=False)
b0, b = df.get_dielectric_function(filename=None)
df.check_sum_rule(b.imag)
equal(b0[0].real, eM1_, 0.01)
atoms.set_calculator(calc)
atoms.get_potential_energy() # get ground state density
# Restart Calculation with fixed density and dense kpoint sampling
calc.set(
kpts={
'density': 15.0,
'gamma': False
}, # dense kpoint sampling
fixdensity=True)
atoms.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=70) # diagonalize Hamiltonian
calc.write('si_large.gpw', 'all') # write wavefunctions
# Getting absorption spectrum
df = DielectricFunction(calc='si_large.gpw', eta=0.05, domega0=0.02, ecut=150)
df.get_dielectric_function(filename='si_abs.csv')
# Getting macroscopic constant
df = DielectricFunction(
calc='si_large.gpw',
frequencies=[0.0],
hilbert=False,
eta=0.0001,
ecut=150,
)
epsNLF, epsLF = df.get_macroscopic_dielectric_constant()
# Make table
epsrefNLF = 14.08 # from [1] in top
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
calc = GPAW('Ag_GLLBSC.gpw', parallel={'domain': 1})
calc.diagonalize_full_hamiltonian(nbands=30)
calc.write('Ag_GLLBSC_full.gpw', 'all')
# Set up dielectric function:
df = DielectricFunction(
calc='Ag_GLLBSC_full.gpw', # Ground state input
domega0=0.05) # energy grid spacing at omega=0
# Momentum transfer, must be the difference between two kpoints!
q_c = [1.0 / 10, 0, 0]
df.get_eels_spectrum(q_c=q_c) # a file called 'eels.csv' is generated
# Plot spectrum
import numpy as np
import matplotlib.pyplot as plt
data = np.loadtxt('eels.csv', delimiter=',')
omega = data[:, 0]
eels = data[:, 2]
plt.plot(omega, eels)
plt.xlabel('Energy (eV)')
plt.ylabel('Loss spectrum')
plt.xlim(0, 20)
plt.show()
calc = GPAW(mode=PW(200),
kpts=(4,4,4),
parallel={'band':1},
idiotproof=False, # allow uneven distribution of k-points
xc='LDA')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('Al', 'all')
t2 = time.time()
# Excited state calculation
q = np.array([1/4.,0.,0.])
w = np.linspace(0, 24, 241)
df = DielectricFunction(calc='Al', frequencies=w, eta=0.2, ecut=50,
hilbert=False)
df.get_eels_spectrum(xc='ALDA', filename='EELS_Al_ALDA',q_c=q)
#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'
world.barrier()
d = np.loadtxt('EELS_Al_ALDA',delimiter=',')
# New results are compared with test values
wpeak1,Ipeak1 = findpeak(d[:,0],d[:,1])
wpeak2,Ipeak2 = findpeak(d[:,0],d[:,2])
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
calc = GPAW("Ag_GLLBSC.gpw")
calc.diagonalize_full_hamiltonian(nbands=30)
calc.write("Ag_GLLBSC_full.gpw", "all")
# Set up dielectric function:
df = DielectricFunction(calc="Ag_GLLBSC_full.gpw", domega0=0.05) # Ground state input # energy grid spacing at omega=0
# Momentum transfer, must be the difference between two kpoints!
q_c = [1.0 / 10, 0, 0]
df.get_eels_spectrum(q_c=q_c) # a file called 'eels.csv' is generated
# Plot spectrum
import numpy as np
import matplotlib.pyplot as plt
data = np.loadtxt("eels.csv", delimiter=",")
omega = data[:, 0]
eels = data[:, 2]
plt.plot(omega, eels)
plt.xlabel("Energy (eV)")
plt.ylabel("Loss spectrum")
plt.xlim(0, 20)
plt.show()
from pathlib import Path
from gpaw.mpi import world
from gpaw.response.df import DielectricFunction
from gpaw.response.qeh import BuildingBlock
df = DielectricFunction(calc='MoS2_gs_fulldiag.gpw',
eta=0.001,
domega0=0.05,
omega2=10.0,
nblocks=8,
ecut=150,
truncation='2D')
buildingblock = BuildingBlock('MoS2', df, qmax=3.0)
buildingblock.calculate_building_block()
if world.rank == 0:
Path('MoS2_gs_fulldiag.gpw').unlink()
from __future__ import print_function
from gpaw.response.df import DielectricFunction
df = DielectricFunction('gs_MoS2.gpw',
ecut=100,
frequencies=(0., ),
nbands=50,
intraband=False,
hilbert=False,
eta=0.1)
alpha = df.get_polarizability(pbc=[True, True, False],
filename=None)[1][0].real
print('alpha = ', alpha, 'AA')
calc = GPAW(mode='pw',
dtype=complex,
xc='RPBE',
nbands=16,
eigensolver='rmm-diis',
occupations=FermiDirac(0.01))
cluster.set_calculator(calc)
cluster.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=24, scalapack=True)
calc.write('Au2.gpw', 'all')
if ABS:
df = DielectricFunction('Au2.gpw',
frequencies=np.linspace(0, 14, 141),
hilbert=not True,
eta=0.1,
ecut=10)
b0, b = df.get_dielectric_function(filename=None,
direction='z')
a0, a = df.get_polarizability(filename=None,
direction='z')
df_ws = DielectricFunction('Au2.gpw',
frequencies=np.linspace(0, 14, 141),
hilbert=not True,
eta=0.1,
ecut=10,
truncation='wigner-seitz')
a0_ws, a_ws = df_ws.get_polarizability(filename=None,
calc = GPAW(mode='pw',
dtype=complex,
xc='RPBE',
nbands=16,
eigensolver='rmm-diis',
occupations=FermiDirac(0.01))
cluster.set_calculator(calc)
cluster.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=24, scalapack=True)
calc.write('Au2.gpw', 'all')
if ABS:
df = DielectricFunction('Au2.gpw',
frequencies=np.linspace(0, 14, 141),
hilbert=not True,
eta=0.1,
ecut=10)
b0, b = df.get_dielectric_function(filename=None,
direction='z')
a0, a = df.get_polarizability(filename=None,
direction='z')
a0_ws, a_ws = df.get_polarizability(filename=None,
wigner_seitz_truncation=True,
direction='z')
w0_ = 5.60491055
I0_ = 244.693028
w_ = 5.696528390
I_ = 207.8
import numpy as np
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
# Part 1: Ground state calculation
atoms = bulk('Si', 'diamond', a=5.431) # Generate diamond crystal structure for silicon
calc = GPAW(mode='pw', 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 = DielectricFunction(calc='si.gpw', # Ground state gpw file (with wavefunction) as input
domega0=0.05) # Using nonlinear frequency grid
df.get_dielectric_function() # By default, a file called 'df.csv' is generated
import numpy as np
from ase.build import bulk
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
# Part 1: Ground state calculation
atoms = bulk('Si', 'diamond',
a=5.431) # Generate diamond crystal structure for silicon
calc = GPAW(mode='pw', 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 = DielectricFunction(
calc='si.gpw', # Ground state gpw file (with wavefunction) as input
domega0=0.05) # Using nonlinear frequency grid
df.get_dielectric_function() # By default, a file called 'df.csv' is generated
