def ascii_file(self, fname='spectrum.dat'):
wf = lib_file.wfile(fname)
wt = lib_file.asciitable(ncol=3)
for i, en in enumerate(self.en):
wt.add_row([en, self.spec[i], self.lam[i]])
wf.write(wt.ret_table())
wf.post(lvprt=1)
def ascii_file(self, fname='spectrum.dat'):
wf = lib_file.wfile(fname)
wt = lib_file.asciitable(ncol=3)
for i, en in enumerate(self.en):
wt.add_row([en, self.spec[i], self.lam[i]])
wf.write(wt.ret_table())
wf.post(lvprt=1)
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).")
