def photoabsorption_spectrum(excitation_list,
spectrum_file=None,
e_min=None,
e_max=None,
delta_e=None,
folding='Gauss',
width=0.1,
comment=None):
"""Uniform absorption spectrum interface
Parameters:
================= ===================================================
``exlist`` ExcitationList
``spectrum_file`` File name for the output file, STDOUT if not given
``e_min`` min. energy, set to cover all energies if not given
``e_max`` max. energy, set to cover all energies if not given
``delta_e`` energy spacing
``energyunit`` Energy unit, default 'eV'
``folding`` Gauss (default) or Lorentz
``width`` folding width in terms of the chosen energyunit
================= ===================================================
all energies in [eV]
"""
spectrum(exlist=excitation_list,
filename=spectrum_file,
emin=e_min,
emax=e_max,
de=delta_e,
energyunit='eV',
folding=folding,
width=width,
comment=comment)
def photoabsorption_spectrum(
excitation_list, spectrum_file=None, e_min=None, e_max=None, delta_e=None, folding="Gauss", width=0.1, comment=None
):
"""Uniform absorption spectrum interface
Parameters:
================= ===================================================
``exlist`` ExcitationList
``spectrum_file`` File name for the output file, STDOUT if not given
``e_min`` min. energy, set to cover all energies if not given
``e_max`` max. energy, set to cover all energies if not given
``delta_e`` energy spacing
``energyunit`` Energy unit, default 'eV'
``folding`` Gauss (default) or Lorentz
``width`` folding width in terms of the chosen energyunit
================= ===================================================
all energies in [eV]
"""
spectrum(
exlist=excitation_list,
filename=spectrum_file,
emin=e_min,
emax=e_max,
de=delta_e,
energyunit="eV",
folding=folding,
width=width,
comment=comment,
)
# folder function
for name in ['Gauss', 'Lorentz']:
folder = Folder(width, name)
x = [0, 2]
y = [[2, 0, 1], [1, 1, 1]]
xl, yl = folder.fold(x, y, dx=.7)
# check first value
if name == 'Lorentz':
func = Lorentz(width)
else:
func = Gauss(width)
yy = np.dot(np.array(y)[:, 0], func.get(xl[0] - np.array(x)))
equal(yl[0, 0], yy, 1.e-15)
# write spectrum
from gpaw.lrtddft import LrTDDFT
from gpaw.lrtddft.spectrum import spectrum
fname = 'lr.dat.gz'
if os.path.exists(fname):
lr = LrTDDFT(fname)
lr.diagonalize()
spectrum(lr, 'spectrum.dat')
def check_convergence(
lr, # LrTDDFT object
dirname='conv', # directory name to store the files
title=None, # title for gnuplot
dn=None, # steps to vary istart/jend
dE=None, # steps to vary energy range
emin=None,
emax=None,
folding='Gauss',
istart=None,
jend=None,
width=0.03): # Gauss/Lorentz width
"""Study the convergence of a LrTDDFT calcualtion by varying istart/jend.
A gnuplot file will be created with the name 'dirname'/conv.gpl."""
if istart is None:
istart0 = lr.kss.istart
else:
if istart < lr.kss.istart:
raise RuntimeError
istart0 = istart
if jend is None:
jend0 = lr.kss.jend
else:
if jend > lr.kss.jend:
raise RuntimeError
jend0 = jend
# create subdirectory for the files
if not os.path.isdir(dirname):
if not os.path.exists(dirname):
os.makedirs(dirname)
else:
raise RuntimeError('Can\'t create directory ' + dirname)
def fname(filename):
return dirname + '/' + filename
fgpl = open(fname('conv.gpl'), 'w')
print >> fgpl, 'set xlabel "omega [eV]"'
print >> fgpl, 'set ylabel "Folded osc. strength [1/eV]"'
if not emin:
emin_gpl = '*'
else:
emin_gpl = str(emin)
if not emax:
emax_gpl = '*'
else:
emax_gpl = str(emax)
print >> fgpl, 'set xrange [' + emin_gpl + ':' + emax_gpl + ']'
if title:
print >> fgpl, 'set title "' + str(title) + '"'
# kss
spectrum(lr.kss, fname('kss.dat'), width=width)
spectrum(lr.kss, fname('ksssticks.dat'), folding=None)
# full
lr.diagonalize(istart=istart0, jend=jend0)
spectrum(lr, fname('full.dat'), width=width)
spectrum(lr, fname('fullsticks.dat'), folding=None)
print >> fgpl, 'plot "' + fname('full.dat') + '" t "full" w l lt 1, \\'
print >> fgpl, ' "'+fname('fullsticks.dat')+\
'" u 1:($2*20) t "" w impulses lt 1, \\'
print >> fgpl, ' "' + fname('kss.dat') + '" t "Kohn-Sham" w l lt 2'
print >> fgpl, 'pause -10'
if dn is None:
dn = -istart0 + jend0
dn = int(dn / 10.)
if dE is None:
# vary istart
print >> fgpl, 'plot "'+fname('full.dat')+'" t "istart=' + \
str(istart0) + '" w l lt 1, \\'
for i in range(1, 4):
istart = istart0 + i * dn
lr.diagonalize(istart=istart, jend=jend0)
fn = fname('istart' + str(istart) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "' + fn + '" t "istart=' + str(
istart) + '" w l lt', i + 1,
if i < 3:
print >> fgpl, ', \\',
print >> fgpl
print >> fgpl, 'pause -10'
# vary jend
print >> fgpl, 'plot "'+fname('full.dat')+'" t "jend=' + \
str(jend0) + '" w l lt 1, \\'
for i in range(1, 4):
jend = jend0 - i * dn
lr.diagonalize(jend=jend, istart=istart0)
fn = fname('jend' + str(jend) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "' + fn + '" t "jend=' + str(
jend) + '" w l lt', i + 1,
if i < 3:
print >> fgpl, ', \\',
print >> fgpl
print >> fgpl, 'pause -10'
else:
# vary the enrgy range
max_kss_energy = 0.
for kss in lr.Om.kss:
max_kss_energy = max(max_kss_energy, kss.get_energy() * Hartree)
print >> fgpl, 'plot "'+ fname('full.dat') + '" t "full"' + \
' w l lt 1, \\'
for i in range(1, 4):
max_energy = max_kss_energy - i * dE
lr.diagonalize(energy_range=max_energy)
fn = fname('max_energy' + str(max_energy) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "' + fn + '" t "dE=-' + str(
i * dE) + '" w l lt',
print >> fgpl, i + 1,
if i < 3:
print >> fgpl, ', \\',
print >> fgpl
# plot different directions
print >> fgpl, 'plot "' + fname('full.dat') + '" u 1:3 t "x" w l lt 1, \\'
print >> fgpl, ' "' + fname('full.dat') + '" u 1:4 t "y" w l lt 2, \\'
print >> fgpl, ' "' + fname('full.dat') + '" u 1:5 t "z" w l lt 3'
print >> fgpl, 'pause -10'
fgpl.close()
def check_convergence(lr, # LrTDDFT object
dirname='conv', # directory name to store the files
title=None, # title for gnuplot
dn=None, # steps to vary istart/jend
dE=None, # steps to vary energy range
emin=None,
emax=None,
folding='Gauss',
istart=None,
jend=None,
width=0.03): # Gauss/Lorentz width
"""Study the convergence of a LrTDDFT calcualtion by varying istart/jend.
A gnuplot file will be created with the name 'dirname'/conv.gpl."""
if istart is None:
istart0 = lr.kss.istart
else:
if istart < lr.kss.istart:
raise RuntimeError
istart0 = istart
if jend is None:
jend0 = lr.kss.jend
else:
if jend > lr.kss.jend:
raise RuntimeError
jend0 = jend
# create subdirectory for the files
if not os.path.isdir(dirname):
if not os.path.exists(dirname):
os.makedirs(dirname)
else:
raise RuntimeError('Can\'t create directory '+dirname)
def fname(filename):
return dirname + '/' + filename
fgpl=open(fname('conv.gpl'), 'w')
print >> fgpl, 'set xlabel "omega [eV]"'
print >> fgpl, 'set ylabel "Folded osc. strength [1/eV]"'
if not emin:
emin_gpl='*'
else:
emin_gpl=str(emin)
if not emax:
emax_gpl='*'
else:
emax_gpl=str(emax)
print >> fgpl, 'set xrange [' + emin_gpl + ':' + emax_gpl + ']'
if title:
print >> fgpl, 'set title "' + str(title) + '"'
# kss
spectrum(lr.kss, fname('kss.dat'), width=width)
spectrum(lr.kss, fname('ksssticks.dat'), folding=None)
# full
lr.diagonalize(istart=istart0, jend=jend0)
spectrum(lr, fname('full.dat'), width=width)
spectrum(lr, fname('fullsticks.dat'), folding=None)
print >> fgpl, 'plot "'+fname('full.dat')+'" t "full" w l lt 1, \\'
print >> fgpl, ' "'+fname('fullsticks.dat')+\
'" u 1:($2*20) t "" w impulses lt 1, \\'
print >> fgpl, ' "'+fname('kss.dat')+'" t "Kohn-Sham" w l lt 2'
print >> fgpl, 'pause -10'
if dn is None:
dn= -istart0 + jend0
dn = int(dn / 10.)
if dE is None:
# vary istart
print >> fgpl, 'plot "'+fname('full.dat')+'" t "istart=' + \
str(istart0) + '" w l lt 1, \\'
for i in range(1,4):
istart = istart0 + i * dn
lr.diagonalize(istart=istart, jend=jend0)
fn= fname('istart' + str(istart) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "'+fn+'" t "istart='+str(istart)+'" w l lt',i+1,
if i < 3:
print >> fgpl,', \\',
print >> fgpl
print >> fgpl, 'pause -10'
# vary jend
print >> fgpl, 'plot "'+fname('full.dat')+'" t "jend=' + \
str(jend0) + '" w l lt 1, \\'
for i in range(1,4):
jend = jend0 - i * dn
lr.diagonalize(jend=jend, istart=istart0)
fn = fname('jend' + str(jend) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "'+fn+'" t "jend='+str(jend)+'" w l lt',i+1,
if i < 3:
print >> fgpl,', \\',
print >> fgpl
print >> fgpl, 'pause -10'
else:
# vary the enrgy range
max_kss_energy = 0.
for kss in lr.Om.kss:
max_kss_energy = max(max_kss_energy, kss.get_energy() * Hartree)
print >> fgpl, 'plot "'+ fname('full.dat') + '" t "full"' + \
' w l lt 1, \\'
for i in range(1,4):
max_energy = max_kss_energy - i * dE
lr.diagonalize(energy_range = max_energy)
fn = fname('max_energy' + str(max_energy) + '.dat')
spectrum(lr, fn, width=width)
print >> fgpl, ' "'+ fn + '" t "dE=-'+ str(i * dE) + '" w l lt',
print >> fgpl, i + 1,
if i < 3:
print >> fgpl,', \\',
print >> fgpl
print >> fgpl, 'pause -10'
# plot different directions
print >> fgpl, 'plot "' + fname('full.dat') + '" u 1:3 t "x" w l lt 1, \\'
print >> fgpl, ' "' + fname('full.dat') + '" u 1:4 t "y" w l lt 2, \\'
print >> fgpl, ' "' + fname('full.dat') + '" u 1:5 t "z" w l lt 3'
print >> fgpl, 'pause -10'
# plot rotary strength
if lr[0].magn is not None:
print >> fgpl, 'set ylabel "Folded rot. strength [cgs/eV]"'
rotatory_spectrum(lr, fname('rotatory.dat'), width=width)
rotatory_spectrum(lr, fname('rotatory_sticks.dat'), folding=None)
print >> fgpl, 'plot "'+fname('rotatory.dat') + \
'" t "rotatory" w l lt 1, \\'
print >> fgpl, ' "' + fname('rotatory_sticks.dat') + \
'" u 1:($2*20) t "" w impulses lt 1'
print >> fgpl, 'pause -10'
fgpl.close()
