class FeffLdosTest(unittest.TestCase):
filepath1 = os.path.join(test_dir, 'feff.inp')
filepath2 = os.path.join(test_dir, 'ldos')
l = FeffLdos.from_file(filepath1, filepath2)
def test_init(self):
efermi = FeffLdosTest.l.complete_dos.efermi
self.assertEqual(efermi, -11.430,
"Did not read correct Fermi energy from ldos file")
def test_complete_dos(self):
complete_dos = FeffLdosTest.l.complete_dos
self.assertEqual(complete_dos.as_dict()['spd_dos']['S']['efermi'],
-11.430,
"Failed to construct complete_dos dict properly")
def test_as_dict_and_from_dict(self):
l2 = FeffLdosTest.l.charge_transfer_to_string()
d = FeffLdosTest.l.as_dict()
l3 = FeffLdos.from_dict(d).charge_transfer_to_string()
self.assertEqual(l2, l3, "Feffldos to and from dict does not match")
Version: 1.0
Last updated: August, 2012''')
parser.add_argument('filename', metavar='filename', type=str, nargs=1,
help='ldos%% file set to plot')
parser.add_argument('filename1', metavar='filename1', type=str, nargs=1,
help='feff.inp input file ')
parser.add_argument('-s', '--site', dest='site', action='store_const',
const=True, help='plot site projected DOS')
parser.add_argument('-e', '--element', dest='element', action='store_const',
const=True, help='plot element projected DOS')
parser.add_argument('-o', '--orbital', dest="orbital", action='store_const',
const=True, help='plot orbital projected DOS')
args = parser.parse_args()
f = FeffLdos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i in xrange(len(structure)):
site = structure[i]
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
def test_as_dict_and_from_dict(self):
l2 = FeffLdosTest.l.charge_transfer_to_string()
d = FeffLdosTest.l.as_dict()
l3 = FeffLdos.from_dict(d).charge_transfer_to_string()
self.assertEqual(l2, l3, "Feffldos to and from dict does not match")
def test_to_dict_and_from_dict(self):
l2 = FeffLdosTest.l.charge_transfer_to_string()
d = FeffLdosTest.l.to_dict
l3 = FeffLdos.from_dict(d).charge_transfer_to_string()
self.assertEqual(l2, l3,
"Feffldos to and from dict does not match")
help='plot site projected DOS')
parser.add_argument('-e',
'--element',
dest='element',
action='store_const',
const=True,
help='plot element projected DOS')
parser.add_argument('-o',
'--orbital',
dest="orbital",
action='store_const',
const=True,
help='plot orbital projected DOS')
args = parser.parse_args()
f = FeffLdos.from_file(args.filename1[0], args.filename[0])
dos = f.complete_dos
all_dos = OrderedDict()
all_dos['Total'] = dos
structure = f.complete_dos.structure
if args.site:
for i in xrange(len(structure)):
site = structure[i]
all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if args.element:
all_dos.update(dos.get_element_dos())
if args.orbital:
def feff_ldos(self,option):
"""
Plot feff LDOS density of states from ldos.dat files
Args:
option:
specifies whether plot by -s(site), -e(element), -o(orbital)
"""
file_name=tkFileDialog.askopenfilename(**self.file_opt)
if file_name == '' or file_name==():
return
self.xmu_ent.delete(0, END)
self.xmu_ent.insert(0, file_name)
file_type = file_name.split(".")[-1]
if file_type == 'dat':
directory = ''
directory_list = file_name.split('/')
for dir in directory_list[:-1]:
directory = directory + '/' +dir
directory = directory[1:]
file_name=file_name[:-6]
feffinpfile = directory + '/feff.inp'
p = FeffLdos.from_file(feffinpfile, file_name)
dos = p.complete_dos
self.all_dos = OrderedDict()
self.all_dos['Total'] = dos
structure = p.complete_dos.structure
if option == '-s':
for i in xrange(len(structure)):
site = structure[i]
self.all_dos['Site ' + str(i) + " " + site.specie.symbol] = \
dos.get_site_dos(site)
if option == '-e':
self.all_dos.update(dos.get_element_dos())
if option == '-o':
self.all_dos.update(dos.get_spd_dos())
#display
keys = self.all_dos.keys()
for label in keys:
energies = self.all_dos[label].energies - self.all_dos[label].efermi
densities = self.all_dos[label].densities
efermi = self.all_dos[label].efermi
self._doses[label] = {'energies': energies, 'densities': densities,
'efermi': efermi}
y = None
alldensities = []
allenergies = []
"""
Note that this complicated processing of energies is to allow for
stacked plots in matplotlib.
"""
for key, dos in self._doses.items():
energies = dos['energies']
densities = dos['densities']
if not y:
y = {Spin.up: np.zeros(energies.shape),
Spin.down: np.zeros(energies.shape)}
newdens = {}
for spin in [Spin.up, Spin.down]:
if spin in densities:
if self.stack:
y[spin] += densities[spin]
newdens[spin] = y[spin].copy()
else:
newdens[spin] = densities[spin]
allenergies.append(energies)
alldensities.append(newdens)
keys = list(self.all_dos.keys())
keys.reverse()
alldensities.reverse()
allenergies.reverse()
allpts = []
for i, key in enumerate(keys):
x = []
y = []
for spin in [Spin.up, Spin.down]:
if spin in alldensities[i]:
densities = list(int(spin) * alldensities[i][spin])
energies = list(allenergies[i])
if spin == Spin.down:
energies.reverse()
densities.reverse()
x.extend(energies)
y.extend(densities)
allpts.extend(zip(x, y))
if self.stack:
self.plt.fill(x, y, color=self.color_order[i % len(self.color_order)],
label=str(key))
else:
self.plt.plot(x, y, color=self.color_order[i % len(self.color_order)],
label=str(key))
if not self.zero_at_efermi:
ylim = self.plt.ylim()
self.plt.plot([self._doses[key]['efermi'],
self._doses[key]['efermi']], ylim,
self.color_order[i % 4] + '--', linewidth=2)
self.plt.set_xlabel('Energies (eV)')
self.plt.set_ylabel('Density of states')
self.fontp.set_size('x-small')
self.plt.legend(prop=self.fontp, loc=0)
self.canvas.show()
else:
tkMessageBox.showerror(title = "feff_ldos by site", message = "Must select Ldos.dat file")
self.xmu_ent.delete(0, Tk.END)
