def pre(self, ofile=None):
self.jmfile = open("%s_jmol.spt"%self.name,'w')
if not ofile==None:
self.jmfile.write('load %s FILTER "nosort"\n'%ofile)
self.jmfile.write ('mo titleformat ""\n\n')
self.jmfile.write('background white\nmo fill\nmo cutoff 0.04\n')
self.htmlfile = lib_file.htmlfile("%s.html"%self.name)
self.htmlfile.pre(self.name)
def pre(self, ofile=None):
self.jmfile = open("%s_jmol.spt" % self.name, 'w')
if not ofile == None:
self.jmfile.write('load %s FILTER "nosort"\n' % ofile)
self.jmfile.write('mo titleformat ""\n\n')
self.jmfile.write('background white\nmo fill\nmo cutoff 0.04\n')
self.htmlfile = lib_file.htmlfile("%s.html" % self.name)
self.htmlfile.pre(self.name)
def run():
print('jmol_MOs.py [<mldfile> [<mldfile2> ...]]\n')
mldfiles = sys.argv[1:]
if len(mldfiles) == 0:
print("No file specified, generating generic script")
mldfiles = ['']
pref = ''
elif len(mldfiles) == 1:
print("Analyzing the file:", mldfiles[0])
pref = mldfiles[0] + '.'
else:
print("Analyzing the files:", mldfiles)
pref = 'multi.'
jopt = jmol_options('jmol.in')
jopt.jmol_input()
jo = lib_file.wfile('%sjmol_orbitals.spt'%pref)
ho = lib_file.htmlfile('%sorbitals.html'%pref)
lo = lib_file.latexfile('%sorbitals.tex'%pref)
ho.pre('Orbitals')
lo.pre(None, graphicx=True)
for mldfile in mldfiles:
print('Analyzing %s ...\n'%mldfile)
if jopt['spec'] == 'sten':
moc = mocoll(jopt['st_ind'], jopt['en_ind'], mldfile)
elif jopt['spec'] == 'frontier':
moc = mocollf(jopt['en_ind'], mldfile)
elif jopt['spec'] == 'occ':
moc = mocoll_occ(jopt['occmin'], jopt['occmax'], mldfile)
else:
raise error_handler.ElseError(self['spec'], 'spec')
moout = mo_output_jmol(moc, jopt)
moout.output(jo)
moh = mo_output_html(moc, jopt)
moh.output(ho)
mol = mo_output_tex(moc, jopt)
mol.output(lo)
jo.post(lvprt=1)
if mldfiles == [""]:
print(" -> Open the Molden-file in jmol and execute the commands contained in this file.")
else:
print(" -> Now simply run \"jmol -n %s\" to plot all the orbitals.\n"%jo.name)
ho.post(lvprt=1)
print(" -> View in browser.")
lo.post(lvprt=1)
print(" -> Compile with pdflatex (or adjust first).")
def plot(self):
"""
Create the plots.
For this purpose, self.data has to be rearranged.
"""
try:
import matplotlib
matplotlib.use('Agg')
import pylab
except:
print("pylab/matplotlib not installed - plotting not possible")
raise
hfname = 'graphs.html'
hfile = lib_file.htmlfile(hfname)
hfile.pre('Property graphs')
htable = lib_file.htmltable(ncol=4)
#set1 = self.data[0][self['state_labels'][0]] # not used anywhere??
matplotlib.rc('font', size=self['fsize'])
for key in self.main_header[1:]:
if key == 'fname': continue
print('Plotting %s ...'%key)
pylab.figure(figsize=(6,4))
for state in self['state_labels']:
ylist = []
for iana_dir in range(len(self['ana_dirs'])):
try:
ylist.append(self.data[iana_dir][state][key])
except KeyError:
print(" ... not able to plot %s for %s."%(key, state))
break
else:
pylab.plot(list(range(len(ylist))), ylist, 'x-', label=state)
pylab.title(key)
numx = len(self['ana_dirs'])
pylab.xticks(range(numx), self['ana_dirs'], rotation=30)
#pylab.margins(0.20)
pylab.subplots_adjust(bottom=0.15)
pylab.xlim((-0.5, numx+1.5))
pylab.ylabel(key)
pylab.legend()
pname = '%s.%s'%(key, self['output_format'])
pylab.savefig(pname)
tel = '<img src="%s", border="1" width="400">'%pname
htable.add_el(tel)
hfile.write(htable.ret_table())
hfile.post()
print(" HTML file %s containing the property graphs written."%hfname)
def plot(self):
"""
Create the plots.
For this purpose, self.data has to be rearranged.
"""
try:
import matplotlib
matplotlib.use('Agg')
import pylab
except:
print("pylab/matplotlib not installed - plotting not possible")
raise
hfname = 'graphs.html'
hfile = lib_file.htmlfile(hfname)
hfile.pre('Property graphs')
htable = lib_file.htmltable(ncol=4)
#set1 = self.data[0][self['state_labels'][0]] # not used anywhere??
matplotlib.rc('font', size=self['fsize'])
for key in self.main_header[1:]:
if key == 'fname': continue
print('Plotting %s ...' % key)
pylab.figure(figsize=(6, 4))
for state in self['state_labels']:
ylist = []
for iana_dir in range(len(self['ana_dirs'])):
try:
ylist.append(self.data[iana_dir][state][key])
except KeyError:
print(" ... not able to plot %s for %s." %
(key, state))
break
else:
pylab.plot(list(range(len(ylist))),
ylist,
'x-',
label=state)
pylab.title(key)
numx = len(self['ana_dirs'])
pylab.xticks(range(numx), self['ana_dirs'], rotation=30)
#pylab.margins(0.20)
pylab.subplots_adjust(bottom=0.15)
pylab.xlim((-0.5, numx + 1.5))
pylab.ylabel(key)
pylab.legend()
pname = '%s.%s' % (key, self['output_format'])
pylab.savefig(pname)
tel = '<img src="%s", border="1" width="400">' % pname
htable.add_el(tel)
hfile.write(htable.ret_table())
hfile.post()
print(" HTML file %s containing the property graphs written." % hfname)
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'])
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']:
vmax = self['vmax']
else:
vmax = state['OmFrag'].max()
pylab.figure(figsize=(2,2))
pylab.pcolor(plot_arr, cmap=pylab.get_cmap(name=self['cmap']), vmin=0., vmax=vmax)
if self['axis']:
pylab.axis('on')
if self['ticks']:
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.savefig(pname, dpi=self['plot_dpi'])
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=(2,2))
ax = pylab.axes()
ax.arrow(0.15, 0.15, 0.5, 0., head_width=0.05, head_length=0.1, fc='k', ec='k')
ax.text(0.20, 0.05, 'hole')
ax.arrow(0.15, 0.15, 0., 0.5, head_width=0.05, head_length=0.1, fc='k', ec='k')
ax.text(0.02, 0.20, 'electron', rotation='vertical')
if self['sscale']:
# pylab.figure(figsize=(2,2))
pylab.pcolor(numpy.zeros([1, 1]), cmap=pylab.get_cmap(name=self['cmap']), vmin=0., vmax=self.maxOm)
pylab.colorbar()
pylab.axis('off')
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)
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'])
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']:
vmax = self['vmax']
else:
vmax = state['OmFrag'].max()
pylab.figure(figsize=(2, 2))
pylab.pcolor(plot_arr,
cmap=pylab.get_cmap(name=self['cmap']),
vmin=0.,
vmax=vmax)
if self['axis']:
pylab.axis('on')
if self['ticks']:
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.savefig(pname, dpi=self['plot_dpi'])
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=(2, 2))
ax = pylab.axes()
ax.arrow(0.15,
0.15,
0.5,
0.,
head_width=0.05,
head_length=0.1,
fc='k',
ec='k')
ax.text(0.20, 0.05, 'hole')
ax.arrow(0.15,
0.15,
0.,
0.5,
head_width=0.05,
head_length=0.1,
fc='k',
ec='k')
ax.text(0.02, 0.20, 'electron', rotation='vertical')
if self['sscale']:
# pylab.figure(figsize=(2,2))
pylab.pcolor(numpy.zeros([1, 1]),
cmap=pylab.get_cmap(name=self['cmap']),
vmin=0.,
vmax=self.maxOm)
pylab.colorbar()
pylab.axis('off')
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)