def test_as_dict_and_from_dict(self):
filepath1 = os.path.join(test_dir, "xmu.dat")
filepath2 = os.path.join(test_dir, "feff.inp")
x = Xmu.from_file(filepath1, filepath2)
data = x.data.tolist()
d = x.as_dict()
x2 = Xmu.from_dict(d)
data2 = x2.data.tolist()
self.assertEqual(data, data2, "Xmu to and from dict does not match")
def test_as_dict_and_from_dict(self):
filepath1 = os.path.join(test_dir, 'xmu.dat')
filepath2 = os.path.join(test_dir, 'feff.inp')
x = Xmu.from_file(filepath1, filepath2)
data=x.data.tolist()
d=x.as_dict()
x2 = Xmu.from_dict(d)
data2= x2.data.tolist()
self.assertEqual(data, data2, "Xmu to and from dict does not match")
def main():
"""
Main function.
"""
parser = argparse.ArgumentParser(description="""
Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013""")
parser.add_argument("filename",
metavar="filename",
type=str,
nargs=1,
help="xmu file to plot")
parser.add_argument(
"filename1",
metavar="filename1",
type=str,
nargs=1,
help="feff.inp filename to import",
)
plt = pretty_plot(12, 8)
color_order = ["r", "b", "g", "c", "k", "m", "y"]
args = parser.parse_args()
xmu = Xmu.from_file(args.filename[0], args.filename1[0])
data = xmu.as_dict()
plt.title(data["calc"] + " Feff9.6 Calculation for " + data["atom"] +
" in " + data["formula"] + " unit cell")
plt.xlabel("Energies (eV)")
plt.ylabel("Absorption Cross-section")
x = data["energies"]
y = data["scross"]
tle = "Single " + data["atom"] + " " + data["edge"] + " edge"
plt.plot(x, y, color_order[1 % 7], label=tle)
y = data["across"]
tle = data["atom"] + " " + data["edge"] + " edge in " + data["formula"]
plt.plot(x, y, color_order[2 % 7], label=tle)
plt.legend()
leg = plt.gca().get_legend()
ltext = leg.get_texts() # all the text.Text instance in the legend
plt.setp(ltext, fontsize=15)
plt.tight_layout()
plt.show()
def main():
"""
Main function.
"""
parser = argparse.ArgumentParser(description='''
Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013''')
parser.add_argument('filename',
metavar='filename',
type=str,
nargs=1,
help='xmu file to plot')
parser.add_argument('filename1',
metavar='filename1',
type=str,
nargs=1,
help='feff.inp filename to import')
plt = pretty_plot(12, 8)
color_order = ['r', 'b', 'g', 'c', 'k', 'm', 'y']
args = parser.parse_args()
xmu = Xmu.from_file(args.filename[0], args.filename1[0])
data = xmu.to_dict
plt.title(data['calc'] + ' Feff9.6 Calculation for ' + data['atom'] +
' in ' + data['formula'] + ' unit cell')
plt.xlabel('Energies (eV)')
plt.ylabel('Absorption Cross-section')
x = data['energies']
y = data['scross']
tle = 'Single ' + data['atom'] + ' ' + data['edge'] + ' edge'
plt.plot(x, y, color_order[1 % 7], label=tle)
y = data['across']
tle = data['atom'] + ' ' + data['edge'] + ' edge in ' + data['formula']
plt.plot(x, y, color_order[2 % 7], label=tle)
plt.legend()
leg = plt.gca().get_legend()
ltext = leg.get_texts() # all the text.Text instance in the legend
plt.setp(ltext, fontsize=15)
plt.tight_layout()
plt.show()
def parse_spectrum(output: str,
feff_inp: str = '',
kind='2dcsv',
*args,
**kwargs):
"""
Open a spectrum file with x as the first column
and y as the second
:param feff_inp:
:param output:
:param kind: default, 2-dimensional comma separated values
:return:
"""
if kind == '2dcsv':
values = loadtxt(fname=output, *args, **kwargs)
return XAS_Spectrum(x=values[:, 1], y=values[:, 0])
if kind == '2dcsv_spec':
values = loadtxt(fname=output, *args, **kwargs)
return XAS_Spectrum(x=values[:, 0], y=values[:, 1])
if kind == 'feff_mu':
xmu = Xmu.from_file(output, feff_inp)
return XAS_Spectrum(x=xmu.energies, y=xmu.mu)
if kind == 'json':
line = open(output, 'r').readline().strip()
xas = loads(line)
return XAS_Spectrum.from_dict(xas)
else:
raise NotImplementedError("Type of data file not found")
def main():
parser = argparse.ArgumentParser(description='''
Convenient DOS Plotter for Feff runs.
Author: Alan Dozier
Version: 1.0
Last updated: April, 2013''')
parser.add_argument('filename', metavar='filename', type=str, nargs=1,
help='xmu file to plot')
parser.add_argument('filename1', metavar='filename1', type=str, nargs=1,
help='feff.inp filename to import')
plt = get_publication_quality_plot(12, 8)
color_order = ['r', 'b', 'g', 'c', 'k', 'm', 'y']
args = parser.parse_args()
xmu = Xmu.from_file(args.filename[0], args.filename1[0])
data = xmu.to_dict
plt.title(data['calc'] + ' Feff9.6 Calculation for ' + data['atom'] + ' in ' +
data['formula'] + ' unit cell')
plt.xlabel('Energies (eV)')
plt.ylabel('Absorption Cross-section')
x = data['energies']
y = data['scross']
tle = 'Single ' + data['atom'] + ' ' + data['edge'] + ' edge'
plt.plot(x, y, color_order[1 % 7], label=tle)
y = data['across']
tle = data['atom'] + ' ' + data['edge'] + ' edge in ' + data['formula']
plt.plot(x, y, color_order[2 % 7], label=tle)
plt.legend()
leg = plt.gca().get_legend()
ltext = leg.get_texts() # all the text.Text instance in the legend
plt.setp(ltext, fontsize=15)
plt.tight_layout()
plt.show()
def test_init(self):
filepath1 = os.path.join(test_dir, "xmu.dat")
filepath2 = os.path.join(test_dir, "feff.inp")
x = Xmu.from_file(filepath1, filepath2)
self.assertEqual(x.absorbing_atom, "O", "failed to read xmu.dat file properly")
def test_init(self):
filepath1 = os.path.join(test_dir, 'xmu.dat')
filepath2 = os.path.join(test_dir, 'feff.inp')
x = Xmu.from_file(filepath1, filepath2)
self.assertEqual(x.absorbing_atom, 'O',
"failed to read xmu.dat file properly")