def generate_diffraction_plot(args):
s = Structure.from_file(args.filenames[0])
c = XRDCalculator()
if args.outfile:
c.get_xrd_plot(s).savefig(args.outfile[0])
else:
c.show_xrd_plot(s)
def generate_diffraction_plot(args):
s = Structure.from_file(args.filenames[0])
c = XRDCalculator()
if args.outfile:
c.get_xrd_plot(s).savefig(args.outfile[0])
else:
c.show_xrd_plot(s)
def test_get_xrd_data(self):
s = self.get_structure("CsCl")
c = XRDCalculator()
xrd = c.get_xrd_pattern(s, two_theta_range=(0, 90))
# Check the first two peaks
self.assertAlmostEqual(xrd.x[0], 21.107738329639844)
self.assertAlmostEqual(xrd.y[0], 36.483184003748946)
self.assertEqual(xrd.hkls[0], {(1, 0, 0): 6})
self.assertAlmostEqual(xrd.d_hkls[0], 4.2089999999999996)
self.assertAlmostEqual(xrd.x[1], 30.024695921112777)
self.assertAlmostEqual(xrd.y[1], 100)
self.assertEqual(xrd.hkls[1], {(1, 1, 0): 12})
self.assertAlmostEqual(xrd.d_hkls[1], 2.976212442014178)
s = self.get_structure("LiFePO4")
xrd = c.get_xrd_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 17.03504233621785)
self.assertAlmostEqual(xrd.y[1], 50.400928948337075)
s = self.get_structure("Li10GeP2S12")
xrd = c.get_xrd_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[1], 14.058274883353876)
self.assertAlmostEqual(xrd.y[1], 4.4111123641667671)
# Test a hexagonal structure.
s = self.get_structure("Graphite")
xrd = c.get_xrd_pattern(s, two_theta_range=(0, 90))
self.assertAlmostEqual(xrd.x[0], 26.21057350859598)
self.assertAlmostEqual(xrd.y[0], 100)
self.assertAlmostEqual(len(list(xrd.hkls[0].keys())[0]), 4)
# Add test case with different lengths of coefficients.
# Also test d_hkl.
coords = [[0.25, 0.25, 0.173], [0.75, 0.75, 0.827], [0.75, 0.25, 0],
[0.25, 0.75, 0], [0.25, 0.25, 0.676], [0.75, 0.75, 0.324]]
sp = ["Si", "Si", "Ru", "Ru", "Pr", "Pr"]
s = Structure(Lattice.tetragonal(4.192, 6.88), sp, coords)
xrd = c.get_xrd_pattern(s)
self.assertAlmostEqual(xrd.x[0], 12.86727341476735)
self.assertAlmostEqual(xrd.y[0], 31.448239816769796)
self.assertAlmostEqual(xrd.d_hkls[0], 6.88)
self.assertEqual(len(xrd), 42)
xrd = c.get_xrd_pattern(s, two_theta_range=[0, 60])
self.assertEqual(len(xrd), 18)
# Test with and without Debye-Waller factor
tungsten = Structure(Lattice.cubic(3.1653), ["W"] * 2,
[[0, 0, 0], [0.5, 0.5, 0.5]])
xrd = c.get_xrd_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2414237.5633093244)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c = XRDCalculator(debye_waller_factors={"W": 0.1526})
xrd = c.get_xrd_pattern(tungsten, scaled=False)
self.assertAlmostEqual(xrd.x[0], 40.294828554672264)
self.assertAlmostEqual(xrd.y[0], 2377745.2296686019)
self.assertAlmostEqual(xrd.d_hkls[0], 2.2382050944897789)
c.get_xrd_plot(tungsten)
def calculate_xrd(request):
results = {}
xrd = XRDCalculator(symprec=0.01)
for name, f in request.FILES.items():
name, s = get_structure(f)
plt = xrd.get_xrd_plot(s, annotate_peaks=False)
fig = plt.gcf()
fig.set_dpi(100)
fig.set_size_inches(8, 6)
ax = plt.gca()
plt.setp(ax.get_xticklabels(), fontsize=16)
plt.setp(ax.get_yticklabels(), fontsize=16)
ax.xaxis.label.set_size(16)
ax.yaxis.label.set_size(16)
si = StringIO()
plt.savefig(si, format="svg")
results[name] = si.getvalue()
return results
# wave = One of [Cuka, AgKa, MoKa, FeKa]
p = Poscar.from_file(os.path.join(poscar_dir, "POSCAR"),
check_for_POTCAR=False)
lattice = p.structure.lattice
species = p.structure.species
frac_coords = p.structure.frac_coords
structure = Structure(lattice, species, frac_coords)
plt = pretty_plot(16, 14)
ax = plt.gca()
c_cuka = XRDCalculator("CuKa")
d1 = c_cuka.get_xrd_plot(structure,
two_theta_range=(0, 100),
annotate_peaks=False,
ax=ax)
d1.savefig(os.path.join(dest_dir, "xrd_CuKa.png"))
c_agka = XRDCalculator("AgKa")
d2 = c_agka.get_xrd_plot(structure,
two_theta_range=(0, 100),
annotate_peaks=False,
ax=ax)
d2.savefig(os.path.join(dest_dir, "xrd_AgKa.png"))
c_moka = XRDCalculator("MoKa")
d3 = c_moka.get_xrd_plot(structure,
two_theta_range=(0, 100),
annotate_peaks=False,
ax=ax)
def get_xrd_plot(args):
s = Structure.from_file(args.xrd_structure_file)
c = XRDCalculator()
return c.get_xrd_plot(s)
def get_xrd_plot(args):
s = Structure.from_file(args.xrd)
c = XRDCalculator()
return c.get_xrd_plot(s)
