def plot(self, xunit=1, pname='spectrum.png', lvprt=1, weight=1):
pylab.figure(figsize=(8, 6))
if xunit.lower() == 'ev':
xlist = self.en
pylab.xlabel('Energy (eV)')
plot_sticks = self.sticks
(xmin, xmax) = (self.emin, self.emax)
elif xunit.lower() == 'nm':
xfac = units.energy['nm'] * units.energy['eV']
xlist = self.lam
#pylab.xlabel(r'$\lambda$') not working ...
pylab.xlabel('Wavelength (nm)')
plot_sticks = [(A, xfac / x0) for A, x0 in self.sticks]
(xmin, xmax) = (xfac / self.emin, xfac / self.emax)
elif xunit.lower() == 'rcm':
xfac = 1. / units.energy['eV'] * units.energy['rcm']
xlist = [en * xfac for en in self.en]
pylab.xlabel('Wavenumber (1/cm)')
plot_sticks = [(A, x0 * xfac) for A, x0 in self.sticks]
(xmin, xmax) = (self.emin * xfac, self.emax * xfac)
else:
raise error_handler.ElseError('xunit', xunit)
pylab.ylabel('Oscillator strength')
if weight == 1:
pylab.plot(xlist, self.spec / max(self.spec), 'k-')
for A, x0 in plot_sticks:
pylab.plot([x0, x0], [-1., A], 'rx-')
elif weight == 2:
pylab.plot(xlist, self.dos / max(self.dos), 'k-')
else:
raise error_handler.ElseError('weight', weight)
pylab.axis(xmin=xmin, xmax=xmax, ymin=0., ymax=1.)
pylab.savefig(pname)
if lvprt >= 1:
print("Spectrum file %s created." % pname)
def write_table(self):
sfile = lib_file.summ_file(self['ana_file'])
header = sfile.ret_header()
ddict = sfile.ret_ddict()
state_labels = sfile.ret_state_labels()
if self['prop_list'] == []:
self['prop_list'] = header[1:]
if self['output_format'] == 'html':
wfile = lib_file.htmlfile
wtable = lib_file.htmltable
elif self['output_format'] == 'latex':
wfile = lib_file.latexfile
wtable = lib_file.latextable
else:
raise error_handler.ElseError(self['output_format'],
'output_format')
wf = wfile(self['fname'])
wf.pre(title='TheoDORE data')
wt = wtable(ncol=len(self['prop_list']) + 1)
wt.add_row(['State'] + self['prop_list'])
for state in state_labels:
if not self['lformula']:
wt.add_el(state)
else:
wt.add_el('$%s$' % (state.replace('(', '^').replace(')', '')))
for prop in self['prop_list']:
try:
wt.add_el(self['fformat'] % ddict[state][prop])
except KeyError:
wt.add_el('-')
wf.write(wt.ret_table())
wf.post(lvprt=1)
#--------------------------------------------------------------------------#
# Parsing and computations
#--------------------------------------------------------------------------#
ifile = 'dens_ana.in'
arg = sys.argv.pop(0)
while len(sys.argv) > 0:
arg = sys.argv.pop(0)
if arg in ["-h", "-H", "--help"]:
ihelp()
elif arg == '-ifile' or arg == '-f':
ifile = sys.argv.pop(0)
else:
raise error_handler.ElseError(arg, 'command line option')
if not os.path.exists(ifile):
print('Input file %s not found!' % ifile)
print(
'Please create this file using theoinp or specify its location using -ifile\n'
)
ihelp()
ioptions = input_options.tden_ana_options(ifile)
theo_header.print_header('Transition density matrix analysis',
ioptions=ioptions)
tdena = lib_tden.tden_ana(ioptions)
if 'mo_file' in ioptions: tdena.read_mos()
def plot(self):
hfname = 'OmFrag.html'
hfile = lib_file.htmlfile(hfname)
hfile.pre('Electron-hole correlation plots')
hfile.write(
'<h2>Electron-hole correlation plots of the Omega matrices for the individual states.</h2>'
)
htable = lib_file.htmltable(ncol=4)
matplotlib.rc('font', size=self['fsize'])
if self['grid']:
edgecolors = 'k'
else:
edgecolors = None
for state in self.state_list:
if self['plot_type'] == 1:
plot_arr = state['OmFrag']
elif self['plot_type'] == 2:
plot_arr = numpy.sqrt(state['OmFrag'])
else:
raise error_handler.ElseError(str(self['plot_type']),
'plot_type')
if self['sscale']:
vmin = self['vmin']
vmax = self['vmax']
else:
vmin = 0.
vmax = state['OmFrag'].max()
# Completely delete the small elements
# for x in numpy.nditer(plot_arr, op_flags = ['readwrite']):
# if x < vmin:
# x[...] = -1. # numpy.nan
pylab.figure(figsize=(2, 2))
pylab.pcolor(plot_arr,
cmap=pylab.get_cmap(name=self['cmap']),
vmin=vmin,
vmax=vmax,
edgecolors=edgecolors)
# *** Different colouring of different parts ***
# frag_lists = [[0, 2, 4, 6], [1, 3, 5]]
# cmaps = ['Reds', 'Blues']
# OmDim = len(plot_arr)
# for frag in frag_lists:
# tmp_arr = numpy.array([[numpy.nan for i in range(OmDim)] for j in range(OmDim)])
# for i in frag:
# tmp_arr[i,i] = plot_arr[i,i]
# pylab.pcolor(tmp_arr, cmap=pylab.get_cmap(cmaps.pop(0)), vmin=0., vmax=vmax, edgecolors=edgecolors)
if self['axis']:
pylab.axis('on')
if self['ticks']:
pylab.tick_params(which='both', length=0)
if self['cticks']:
pylab.xticks([x + 0.5 for x in range(len(plot_arr))],
self['xticks'])
pylab.yticks([y + 0.5 for y in range(len(plot_arr))],
self['yticks'])
else:
pylab.xticks([x + 0.5 for x in range(len(plot_arr))],
[x + 1 for x in range(len(plot_arr))])
pylab.yticks([y + 0.5 for y in range(len(plot_arr))],
[y + 1 for y in range(len(plot_arr))])
else:
pylab.xticks([])
pylab.yticks([])
else:
pylab.axis('off')
if self['cbar']: pylab.colorbar()
pname = 'pcolor_%s.%s' % (state['name'], self['output_format'])
print("Writing %s ..." % pname)
pylab.tight_layout()
pylab.savefig(pname, dpi=self['plot_dpi'])
pylab.close()
tel = '<img src="%s", border="1" width="200">\n' % pname
tel += '<br>%s' % state['name']
htable.add_el(tel)
# create a plot with the e/h axes and optionally the scale
pylab.figure(figsize=(3, 2))
matplotlib.rc('font', size=14)
ax = pylab.axes()
ax.arrow(0.15,
0.15,
0.5,
0.,
head_width=0.05,
head_length=0.1,
fc='r',
ec='r')
ax.text(0.20, 0.03, 'hole', color='r')
ax.arrow(0.15,
0.15,
0.,
0.5,
head_width=0.05,
head_length=0.1,
fc='b',
ec='b')
ax.text(0.02, 0.20, 'electron', rotation='vertical', color='b')
pylab.axis('off')
if self['sscale']:
pylab.savefig('axes_no.%s' % self['output_format'],
dpi=self['plot_dpi'])
# pylab.figure(figsize=(2,2))
pylab.pcolor(numpy.zeros([1, 1]),
cmap=pylab.get_cmap(name=self['cmap']),
vmin=self['vmin'],
vmax=self['vmax'])
pylab.colorbar()
pylab.savefig('axes.%s' % self['output_format'], dpi=self['plot_dpi'])
tel = '<img src="axes.%s", border="1" width="200">\n' % self[
'output_format']
tel += '<br>Axes / Scale'
htable.add_el(tel)
hfile.write(htable.ret_table())
hfile.post()
print(
" HTML file %s containing the electron-hole correlation plots written."
% hfname)