def plot_bandstructure(self,
filename=None,
filepath=None,
max_min_e=None,
show=False,
save=True,
show_vbm_cbm=True):
if 'bands' in self:
from structure import get_kpath
if filename == None:
filename = 'band_structure.pdf'
if filepath == None:
filepath = os.path.join(self.abspath, filename)
else:
filepath = os.path.join(filepath, filename)
#end if
try:
import matplotlib
gui_envs = ['GTKAgg', 'TKAgg', 'agg', 'Qt4Agg', 'WXAgg']
for gui in gui_envs:
try:
matplotlib.use(gui, warn=False, force=True)
from matplotlib import pyplot
success = True
break
except:
continue
#end try
#end for
from matplotlib.pyplot import figure, plot, xlabel, ylabel, title, show, ylim, legend, xlim, rcParams, rc, savefig, gca, xticks, axvline, scatter
params = {
'legend.fontsize': 14,
'figure.facecolor': 'white',
'figure.subplot.hspace': 0.,
'axes.labelsize': 16,
'xtick.labelsize': 14,
'ytick.labelsize': 14
}
rcParams.update(params)
except (ImportError, RuntimeError):
success = False
if not success:
figure, plot, xlabel, ylabel, title, show, ylim, legend, xlim, rcParams, savefig, bar, xticks, subplot, grid, setp, errorbar, loglog, semilogx, semilogy, text = unavailable(
'matplotlib.pyplot', 'figure', 'plot', 'xlabel', 'ylabel',
'title', 'show', 'ylim', 'legend', 'xlim', 'rcParams',
'savefig', 'bar', 'xticks', 'subplot', 'grid', 'setp',
'errorbar', 'loglog', 'semilogx', 'semilogy', 'text')
#end if
fig = figure()
ax = gca()
kpath = get_kpath(structure=self.input_structure,
check_standard=False)
x = kpath['explicit_path_linearcoords']
labels = kpath['explicit_kpoints_labels']
nbands = self.input.system.nbnd
for nb in range(nbands):
y = []
for bi in self.bands.up:
y.append(bi['eigs'][nb])
#end for
y = array(y) - self.bands.vbm.energy
plot(x, y, 'k')
if len(self.bands.down) > 0:
y = []
for bi in self.bands.down:
y.append(bi['eigs'][nb])
#end for
y = array(y) - self.bands.vbm.energy
plot(x, y, 'r')
#end if
#end for
for ln, li in enumerate(labels):
if li is not '':
axvline(x[ln], ymin=-100, ymax=100, linewidth=3, color='k')
if li == 'GAMMA':
labels[ln] = r'$\Gamma$'
elif li is not '':
labels[ln] = '${0}$'.format(li)
#end if
if labels[ln - 1] is not '' and ln > 0:
labels[ln] = labels[ln - 1] + '|' + labels[ln]
labels[ln - 1] = ''
#end if
#end if
#end for
xlim([min(x), max(x)])
if max_min_e is None:
ylim(-5, +5)
else:
ylim(max_min_e[0], max_min_e[1])
#end if
ylabel('Energy (eV)')
xticks(x, labels)
ax.tick_params(axis='x', which='both', length=0)
ax.tick_params(axis='x', which='both', pad=10)
#end if
if show_vbm_cbm:
vbm = self.bands.vbm
cbm = self.bands.cbm
for kn, ki in enumerate(self.bands.up):
if (vbm.kpoint_rel == ki['kpoint_rel']).all():
scatter(x[kn], 0, c='green', s=100)
#end if
if (cbm.kpoint_rel == ki['kpoint_rel']).all():
scatter(x[kn], cbm.energy - vbm.energy, c='r', s=100)
#end if
#end for
#end if
if save:
savefig(filename, format='pdf', bbox_inches='tight')
#end if
if show:
show()
def post_analyze(self,analyzer):
if not self.has_generic_input():
calctypes = self.input.get_output_info('calctypes')
opt_run = calctypes!=None and 'opt' in calctypes
if opt_run:
opt_file = analyzer.results.optimization.optimal_file
if opt_file is None:
self.failed = True
#end if
#end if
exc_run = 'excitation' in self
if exc_run:
exc_failure = False
edata = self.read_einspline_dat()
exc_input = self.excitation
exc_spin,exc_type,exc_spins,exc_types,exc1,exc2 = check_excitation_type(exc_input)
elns = self.input.get_electron_particle_set()
if exc_type==exc_types.band:
# Band Index 'tw1 band1 tw2 band2'. Eg., '0 45 3 46'
# Check that tw1,band1 is no longer in occupied set
tw1,bnd1 = exc2.split()[0:2]
tw2,bnd2 = exc2.split()[2:4]
if exc1 in ('up','down'):
spin_channel = exc1
dsc = edata[spin_channel]
for idx,(tw,bnd) in enumerate(zip(dsc.TwistIndex,dsc.BandIndex)):
if tw == int(tw1) and bnd == int(bnd1):
# This orbital should no longer be in the set of occupied orbitals
if idx<elns.groups[spin_channel[0]].size:
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, the first orbital \'{} {}\' is still occupied (see einspline file).\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],tw1,bnd1)
exc_failure = True
#end if
elif tw == int(tw2) and bnd == int(bnd2):
# This orbital should be in the set of occupied orbitals
if idx>=elns.groups[spin_channel[0]].size:
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, the second orbital \'{} {}\' is not occupied (see einspline file).\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],tw2,bnd2)
exc_failure = True
#end if
#end if
#end for
else:
self.warn('No check for \'{}\' excitation of type \'{}\' was done. When this path is possible, then a check should be written.'.format(exc_input[0],exc_input[1]))
#end if
elif exc_type in (exc_types.energy,exc_types.lowest):
# Lowest or Energy Index '-orbindex1 +orbindex2'. Eg., '-4 +5'
if exc_type==exc_types.lowest:
if exc_spin==exc_spins.down:
orb1 = elns.groups.d.size
else:
orb1 = elns.groups.u.size
#end if
orb2 = orb1+1
else:
orb1 = int(exc_input[1].split()[0][1:])
orb2 = int(exc_input[1].split()[1][1:])
#end if
if exc1 in ('up','down'):
spin_channel = exc1
nelec = elns.groups[spin_channel[0]].size
eigs_spin = edata[spin_channel].Energy
# Construct the correct set of occupied orbitals by hand based on
# orb1 and orb2 values that were input by the user
excited = eigs_spin
order = eigs_spin.argsort()
ground = excited[order]
# einspline orbital ordering for excited state
excited = excited[:nelec]
# hand-crafted orbital order for excited state
# ground can be list or ndarray, but we'll convert it to list
# so we can concatenate with list syntax
ground = np.asarray(ground).tolist()
# After concatenating, convert back to ndarray
hc_excited = np.array(ground[:orb1-1]+[ground[orb2-1]]+ground[orb1:nelec])
etol = 1e-6
if np.abs(hc_excited-excited).max() > etol:
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, the second orbital \'{}\' is not occupied (see einspline file).\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],orb1)
exc_failure = True
#end if
elif exc1 in ('singlet','triplet'):
wf = self.input.get('wavefunction')
occ = wf.determinantset.multideterminant.detlist.csf.occ
if occ[int(orb1)-1]!='1':
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, this is inconsistent with the occupations in detlist \'{}\'.\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],occ)
exc_failure = True
#end if
if occ[int(orb2)-1]!='1':
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, this is inconsistent with the occupations in detlist \'{}\'.\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],occ)
exc_failure = True
#end if
#end if
else:
# The format is: 'gamma vb z cb'
if exc1 in ('singlet','triplet'):
self.warn('No check for \'{}\' excitation of type \'{}\' was done. When this path is possible, then a check should be written.'.format(exc_input[0],exc_input[1]))
else:
# assume excitation of form 'gamma vb k cb' or 'gamma vb-1 k cb+1'
excitation = exc2.upper().split(' ')
k_1, band_1, k_2, band_2 = excitation
tilematrix = self.system.structure.tilematrix()
wf = self.input.get('wavefunction')
if exc_spin==exc_spins.up:
sdet = wf.determinantset.get('updet')
else:
sdet = wf.determinantset.get('downdet')
#end if
from numpy import linalg,where,isclose
vb = int(sdet.size / abs(linalg.det(tilematrix))) -1 # Separate for each spin channel
cb = vb+1
# Convert band_1, band_2 to band indexes
bands = [band_1, band_2]
for bnum, b in enumerate(bands):
b = b.lower()
if 'cb' in b:
if '-' in b:
b = b.split('-')
bands[bnum] = cb - int(b[1])
elif '+' in b:
b = b.split('+')
bands[bnum] = cb + int(b[1])
else:
bands[bnum] = cb
#end if
elif 'vb' in b:
if '-' in b:
b = b.split('-')
bands[bnum] = vb - int(b[1])
elif '+' in b:
b = b.split('+')
bands[bnum] = vb + int(b[1])
else:
bands[bnum] = vb
#end if
else:
QmcpackInput.class_error('{0} in excitation has the wrong formatting'.format(b))
#end if
#end for
band_1, band_2 = bands
# Convert k_1 k_2 to wavevector indexes
structure = self.system.structure.get_smallest().copy()
structure.change_units('A')
from structure import get_kpath
kpath = get_kpath(structure=structure)
kpath_label = array(kpath['explicit_kpoints_labels'])
kpath_rel = kpath['explicit_kpoints_rel']
k1_in = k_1
k2_in = k_2
if k_1 in kpath_label and k_2 in kpath_label:
k_1 = kpath_rel[where(kpath_label == k_1)][0]
k_2 = kpath_rel[where(kpath_label == k_2)][0]
kpts = structure.kpoints_unit()
found_k1 = False
found_k2 = False
for knum, k in enumerate(kpts):
if isclose(k_1, k).all():
k_1 = knum
found_k1 = True
#end if
if isclose(k_2, k).all():
k_2 = knum
found_k2 = True
#end if
#end for
if not found_k1 or not found_k2:
QmcpackInput.class_error('Requested special kpoint is not in the tiled cell\nRequested "{}", present={}\nRequested "{}", present={}\nAvailable kpoints: {}'.format(k1_in,found_k1,k2_in,found_k2,sorted(set(kpath_label))))
#end if
else:
QmcpackInput.class_error('Excitation wavevectors are not found in the kpath\nlabels requested: {} {}\nlabels present: {}'.format(k_1,k_2,sorted(set(kpath_label))))
#end if
tw1,bnd1 = (k_1,band_1)
tw2,bnd2 = (k_2,band_2)
spin_channel = exc1
dsc = edata[spin_channel]
for idx,(tw,bnd) in enumerate(zip(dsc.TwistIndex,dsc.BandIndex)):
if tw == int(tw1) and bnd == int(bnd1):
# This orbital should no longer be in the set of occupied orbitals
if idx<elns.groups[spin_channel[0]].size:
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, the first orbital \'{} {}\' is still occupied (see einspline file).\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],tw1,bnd1)
exc_failure = True
#end if
elif tw == int(tw2) and bnd == int(bnd2):
# This orbital should be in the set of occupied orbitals
if idx>=elns.groups[spin_channel[0]].size:
msg = 'WARNING: You requested \'{}\' excitation of type \'{}\',\n'
msg += ' however, the second orbital \'{} {}\' is not occupied (see einspline file).\n'
msg += ' Please check your input.'
msg = msg.format(spin_channel,exc_input[1],tw2,bnd2)
exc_failure = True
#end if
#end if
#end for
#end if
if exc_failure:
self.failed = True
self.warn(msg)
filename = self.identifier+'_errors.txt'
open(os.path.join(self.locdir,filename),'w').write(msg)
